Why were Deuterocanonical books rejected in the Reformation?

It is a very common, but highly misleading claim, to assume that the Reformation had been effectual for the rejection of the Deuterocanonical Books (DB).

When we look at the quantity of books included in Bibles throughout the millennia, we actually notice the opposite, a clear and systematic increase of DB's in the time of the Reformation!

In nearly all discussions, we hear the unreflected argument that e.g. Luther separated those books, what usually silences the listeners. Little to no awareness exists about Luther having given equal weight to the DB's than to the books of James, Hebrews, Jude and Revelation. Another fact usually ignored is that even the Roman Catholic Church made previously a clear distinction between the DB's and the true books of the Bible (although being mainly responsible for the transformation of those books previously read in the churches, into books formally considered in the wider canon).

Most importantly, we rarely reflect on what God actually thinks about the matter - if He would be impressed by such arguments of separate categories. The very probable reality is, that it is entirely irrelevant in God's eyes if those books are in a separate section or merged. Everyone will be held responsible at the Great Judgment who added any word in between 2 covers issued as His Word (not one of the Reformers chose to put the DB's in a separate volume or to simply ignore those, what would have been a real reform). God will not be impressed by human reasoning and excuses.

Source: Apocrypha Timeline of Inclusion & Exclusion

The Protestants rejection of the deuterocanonical books being equal to Holy Scripture is based primarily on Jerome's Helmeted Preface:

Jerome, in his Prologue to the Books of the Kings

This preface to the Scriptures may serve as a helmeted [i.e. defensive] introduction to all the books which we turn from Hebrew into Latin, so that we may be assured that what is outside of them must be placed aside among the Apocryphal writings. Wisdom, therefore, which generally bears the name of Solomon, and the book of Jesus the Son of Sirach, and Judith, and Tobias, and the Shepherd [of Hermes?] are not in the canon. The first book of Maccabees is found in Hebrew, but the second is Greek, as can be proved from the very style.

How did Jerome arrive at this conclusion?

First, he obtained the Hebrew scriptures from the Jews of his day (late fourth century) at great cost.

Jerome, in his Apology Against Rufinus, Book II, Section 35

...my own familiar friend should frankly accept from a Christian and a friend what he has taken great pains to obtain from the Jews and has written down for him at great cost.

He compared these Hebrew scriptures he obtained (an ancestor of the Masoretic text) to the Septuagint (Greek translation of the Old Testament) which was used throughout the Christian Churches.

In this comparison, Jerome found numerous differences. He reasoned that the Jewish copy must be the more accurate of the two, as the Jewish copy was written in Hebrew just like the original Old Testament, while the Septuagint was a translation - and in translating, errors can crop up.

Jerome, in his Preface to Pentateuch

Hear, therefore, O rival; listen, O detractor! I do not condemn, I do not censure the Seventy, but I confidently prefer the Apostles to all of them. Christ speaks to me through their mouth, who I read were placed before the prophets among the Spiritual gifts, among which interpreters hold almost the last place.

This belief that the Septuagint was a poor translation of the Jewish scripture led him to believe that the Septuagint could also have been mistaken in its collection of scriptures, causing Jerome to prefer the shortened Jewish canon over the expanded Septuagint canon.

Additionally, while reviewing the New Testament, Jerome found that where the New Testament quoted the Old Testament in a spot where the Jewish copy and the Septuagint disagreed on the text, the New Testament followed the Jewish copy (and not the Septuagint).

Jerome, in his Apology Against Rufinus, Book II, Section 34

The Hebrew Scriptures are used by apostolic men; they are used, as is evident, by the apostles and evangelists. Our Lord and Savior himself whenever he refers to the Scriptures, takes his quotations from the Hebrew; as in the instance of the words "He that believes in me, as the Scripture has said, out of his belly shall flow rivers of living water," and in the words used on the cross itself, "Eli, Eli, lama sabachthani," which is by interpretation "My God, my God, why have you forsaken me?" not, as it is given by the Septuagint, "My God, my God, look upon me, why have you forsaken me?" and many similar cases. I do not say this in order to aim a blow at the seventy translators; but I assert that the Apostles of Christ have an authority superior to theirs. Wherever the Seventy agree with the Hebrew, the apostles took their quotations from that translation; but, where they disagree, they set down in Greek what they had found in the Hebrew.

This led Jerome to proclaim his great challenge:

Jerome, in his Apology Against Rufinus, Book II, Section 34

And further, I give a challenge to my accuser. I have shown that many things are set down in the New Testament as coming from the older books, which are not to be found in the Septuagint; and I have pointed out that these exist in the Hebrew. Now let him show that there is anything in the New Testament which comes from the Septuagint but which is not found in the Hebrew, and our controversy is at an end.

A brief aside - as it turns out, modern scholarship has found that Jerome was wrong on two counts.

First, the New Testament authors frequently quoted from the Septuagint (against the Masoretic). Examples abound in this article; in Matthew 21:16, Jesus quotes Septuagint's Psalm 8:2 "ordained praise" instead of the differently worded Masoretic Psalm 8:2 "ordained strength", 1 Peter 4:18 follows the Septuagint Proverbs 11:31, and so on. Jerome's challenge was met.

Second, the Dead Sea scrolls showed us that the Septuagint was a good translation of the Pre-Septuagint, a different Hebrew text tradition that pre-dated Jesus, rather than a bad translation of the Proto-Masoretic text as Jerome thought. Jerome was not aware that there were multiple Hebrew text traditions, he only had knowledge of the one he painstaking obtained that the Jews in the late 4th century used. More info on this in this article.

During the Reformation, the fathers of Protestantism followed Jerome's teaching on the Deuterocanonical books.

John Calvin, Acts of the Council of Trent with the Antidote, ON THE FOURTH SESSION

Of their admitting all the Books promiscuously into the Canon, I say nothing more than it is done against the consent of the primitive Church. It is well known what Jerome states as the common opinion of earlier times. And Ruffinus, speaking of the matter as not at all controverted, declares with Jerome that Ecclesiasticus, the Wisdom of Solomon, Tobit, Judith, and the history of the Maccabees, were called by the Fathers not canonical but ecclesiastical books, which might indeed be read to the people, but were not entitled to establish doctrine. I am not, however, unaware that the same view on which the Fathers of Trent now insist was held in the Council of Carthage. The same, too, was followed by Augustine in his Treatise on Christian Doctrine...

This was important to Calvin, because if you admitted those books as part of the Bible canon, then the Romanists can prove purgatory from the bible.

John Calvin, Acts of the Council of Trent with the Antidote, ON THE FOURTH SESSION

Add to this, that they provide themselves with new supports when they give full authority to the Apocryphal books. Out of the second of the Maccabees they will prove Purgatory and the worship of saints; out of Tobit satisfactions, exorcisms, and what not. From Ecclesiasticus they will borrow not a little. For from whence could they better draw their dregs? I am not one of those, however, who would entirely disapprove the reading of those books...

Martin Luther had a similar problem. Early on, he articulated his belief in Sola Scriptura.

Martin Luther, 1521, Diet of Worms

Unless I am convinced by the testimony of the Scriptures or by clear reason (for I do not trust either in the pope or in councils alone, since it is well known that they have often erred and contradicted themselves), I am bound by the Scriptures I have quoted and my conscience is captive to the Word of God.

The immediate problem he discovered was in reconciling what was in the bible with what he believed. What was he to do with the Deuterocanonical books of the Old Testament, which make explicit doctrines like Purgatory? Or what of the New Testament books like James which make clear faith without works is dead?

In 1534, when Luther's Bible translation was published, he moves Deuterocanon to the end of his Old Testament and labels them "Apocrypha".

Apocrypha (Deuterocanon) introduction, Luther’s Bible

These books are not held equal to the Scriptures, but are useful and good to read

Similar to his Apocrypha, he was skeptical of Hebrews, James, Jude and Revelation, and stuck them at the end of his New Testament, saying "Up to this point we have had to do with the true and certain chief books of the New Testament. The four which follow have from ancient times had a different reputation."

Luther's Preface to the Epistle to the Hebrews

Up to this point we have had to do with the true and certain chief books of the New Testament. The four which follow have from ancient times had a different reputation... This seems, as it stands, to be against all the Gospels and St. Paul’s epistles... [The Epistle to the Hebrews] we cannot put it on the same level with the apostolic epistles.

Luther's Preface to the Epistles of St. James and St. Jude

...I do not regard it [the epistle of St. James] as the writing of an apostle; and my reasons follow. In the first place it is flatly against St. Paul and all the rest of Scripture in ascribing justification to works... He mangles the Scriptures and thereby opposes Paul and all Scripture... Therefore, I will not have him in my Bible to be numbered among the true chief books

Luther's Preface to the Epistles of St. James and St. Jude

Concerning the epistle of St. Jude... it is an epistle that need not be counted among the chief books which are supposed to lay the foundations of faith.

Luther's Preface to the Revelation of St. John

About this book of the Revelation of John... it makes me consider it to be neither apostolic nor prophetic... I can in no way detect that the Holy Spirit produced it.

For the books that were problematic to his doctrines, Luther wrote off their importance - his Apocrypha in the Old Testament and his Antilegomena in the New Testament. Neither he nor Calvin dared to remove them from the Bible though, as by their time Christians had these books in their bibles for over a thousand years thanks to the Latin Vulgate. All that could be done was move these books to a section in the back of the bible.

Around 1571 AD, the Protestant Church of England's Thirty-Nine Articles was published which clearly noted the Deuterocanon as part of the scriptures that "the Church doth read for example of life and instruction of manners; but yet it doth not apply them to establish any doctrine".

Between 1642 and 1649 AD, the English civil war broke out. The Long Parliament of 1644 decreed that only the "Hebrew Canon" would be read in the Church of England, and in 1647 the Westminster Confession of Faith was issued which decreed an explicit 39-book OT canon and 27-book NT canon. This Confession is the time when Protestants finally formalize their rejection of the Deuterocanon, and just completely exclude it from the Bible.

And yet... after the end of the English civil war, with the Restoration of the Monarchy to Charles II of England (1660–1685), the Church of England was once again governed by the Thirty-Nine Articles, and thus emphatically maintained that the Deuterocanon is part of the Bible and is to be read with respect by her members (but not used to establish any doctrine).

It wasn't the Reformation that rejected the Deuterocanon. Modern Protestantism, with its complete rejection of the Deuterocanon and lack of those books in their bible, thus descends from the Westminster Confession of Faith and the temporary change in the Church of England that occurred during their civil war - this Protestant distinctive is shared by Presbyterianism and Baptist confessions of faith, among others.

[Note: Above references taken from this article]