In four hours and forty minutes, the fourth seed defeated Rune of Denmark, 4-6 6-1 5-7 7-6 (7-2) 6-2.
It was the second match in three days that concluded at Roland Garros in the wee hours of the morning. On Sunday, at 03:07, Novak Djokovic defeated Lorenzo Musetti in five sets.
In the men’s fourth round, Zverev will take on Alex de Minaur after the Australian defeated Daniil Medvedev, the fifth seed, earlier on Monday.
Champion of the US Open Coco Gauff declared on Sunday that 3 a.m. tennis matches were “unhealthy”.
Rune and Zverev did not start their warm-ups until after 21:00 local time, even though they were scheduled to be on the court at 20:15.
Four hours and forty-nine minutes were spent in the previous encounter between Djokovic and Francisco Cerundolo on the Philippe Chatrier.
Zverev was performing in Paris while the trial over charges of assault against his former girlfriend, which he refutes, was still going on in Berlin.
Zverev, 27, a German, has lost in the semifinals of the last three French Opens and is still chasing his first Grand Slam victory.
13th seed Rune broke him halfway through the opening set.