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Transit is still allowed, according to https://www.iatatravelcentre.com/world.php -> Japan:
- Effective 30 November 2021 until 31 December 2021, passengers are not allowed to enter.
- This does not apply to:
- nationals of Japan;
- passengers with a visa issued by Japan outside Japan.
Note that from what I recall Japan never closed international transit for air travelers because of COVID-19 (unlike e.g. Taiwan), as long as the transit doesn't entail entering Japan.