Were the "Petlurovites" who took Kiev in 1918 commanded by a communist?

Russian Civil War, especially in its early stages, was a time of constantly shifting loyalties and short-lived alliances dictated by short-term considerations. Thus, to correctly evaluate events, one needs to view them in context.

At first, Petlyura indeed was an official of the government led by Vynnychenko. Note that at this point Vynnichenko was a member of Ukrainian Social-Democratic Worker's Party - not a communist. Nevertheless, their views on the future of Ukraine differed drastically - Petlyura aimed for complete independence, while Vynnychenko wanted autonomy within federal Russia (at this point - under the Provisional Government). These two factions would clash constantly over the course of UNR's existence, and only external pressure allowed them to coexist within one government.

Bolshevik Revolution and the starting civil war split these two factions for the first time - Petlyura wanted to fight for independence, while Vynnychenko still wanted to negotiate a peaceful solution. Note that at this point (27th of December, 1917) Bolsheviks already managed to seize control most of the Kharkov governorate. Petlyura tried to mobilise the forces loyal to him against the Bolsheviks anyway; this led to him losing his post as the Minister for abuse of authority. Undaunted, he managed to secure funding from the French to raise a volunteer force with the aim of reclaiming the Bolshevik-controlled territory anyway. These forces were used in suppression of the Kiev Uprising, and then retreated from Kiev along with other UNR forces by Soviet offensive. These are not the Petlurovites in the novel.

At this moment, weakened UNR falls under German control. For a time, Petlyra was aligned with UNR, but after Bolshevik forces were pushed out of Kiev, his nationalist tendencies and known support of Entente often clashes with current government's position, and in March 1918 he is removed from command. In April 1918, Vynnychenko's government is ousted in a coup, and Skoropadsky's govenment is installed. As a known nationalist, Petlyra is arrested in July on charges of conspiracy to overthrow the government.

German-controlled Skoropadsky's government was largely unpopular - so unpopular that by August of 1918 Vynnychenko managed to assemble both right-wing and left-wing parties in a coalition opposing Hetmanate - at this point, nationalist and socialist factions ally again. With Germany losing the war, the government lost its only means of support. Vynnychenko managed to get Petlyura out of the prison and again put him in command of anti-Hetman uprising; and by the end of December 1918 Skoropadsky was defeated - these are the events described in Bulgakov's book; at this point, Vynnychenko is still in Socialist-Democratic Party.

While Vynnychenko was formally the prime minister of Directory, this iteration of UNR was really controlled by Petlyura and his nationalists; the deteriorating situation within the country also led to more radical decisions, in particular, nationalists crack down on Bolshevik and White supporters. In protest against these events, Socialists leave the government, leaving Petlyura a military dictator. At this point Vynnychenko and Petlyra split for the last time - Vynnychenko emigrates to Europe.

While in exile, Vynnychenko tries to play for the winning team - he creates the Foreign Group of Ukrainian Communists, and in 1920 travels to Moscow to negotiate with Sovnarkom... unsuccesfully. Disillusioned, he left Russia never to return. Note that your information of him being a member of Sovnarkom seems to be incorrect.

In conclusion: while Vynnychenko did show willingness to coexist with Bolsheviks, and later in life did try to join them, he can hardly be called a communist at any point where he and Petlyura managed to act in accord. Moreover, whether Vynnychenko really controlled Petlyura and his forces at any given point in time is kind of questionable; rather, their interests managed to coincide during certain periods, and as soon as their interests diverged, whoever had the upper hand at the moment undermined the other. In particular, during the events described in Bulgakov's novel/play Vynnychenko played second fiddle to Petlyura's nationalist faction, and was removed from power almost immediately after Skoropadsky was defeated. Thus, the answer to your question is a resounding "no".