The latest I can remember is the 1997 Coca-Cola 600, which ended around 1:15 am local time (and shortened to 333 laps from 400 due to time issues - otherwise it could have been after 2:00 am if there were a lot of cautions in those final 67 laps - and who knows with exhausted drivers).
Great memory from eleven years ago. That must have been a tough call if it had nothing to do with track conditions.
We had a couple of race threads that ran to the wee hours of the morning.