Defending champion and 24-time Grand Slam title winner Djokovic came from two sets to one down to defeat Lorenzo Musetti 7-5, 6-7 (6/8), 2-6, 6-3, 6-0 in a clash which only started just before 10:45 p.m. (20:45 GMT) on Saturday.
It was easily the latest finish to a French Open tie and came after organisers squeezed in extra matches onto the two main show courts, which both have retractable roofs, to counter the scheduling chaos caused by a seventh day of rain in Paris.
"I don't want to get into this debate," said Djokovic initially before adding: "I think certain things could have been handled differently.
"There is a certain beauty in winning the match at three in the morning if it was the last of the tournament, but this isn't the case."
Djokovic's four-hour 29-minute victory allowed the 37-year-old world number one to equal Roger Federer's record of 369 Grand Slam match wins.
"Physically, I really went to my limits to win this match. When you play rallies of more than 20 shots, at two in the morning.... Who plays at two in the morning?" he added.
"We play few matches in our life at this time. The conditions were very heavy, it was very cold. You didn't have many free points behind your serve."
Djokovic must now recover to face Argentinian 27th seed Francisco Cerundolo in the round of 16 on Monday after avoiding what would have been his earliest exit at the French Open in 15 years.
Despite the late finish in Paris, it is the Australian Open in Melbourne that holds the Grand Slam record - in 2008, Lleyton Hewitt and Marcos Baghdatis played a match until 4:34 a.m.
At the US Open in New York, the latest finish was 2:50 a.m. in 2022 when Carlos Alcaraz defeated Jannik Sinner.
Wimbledon operates an 11 p.m. curfew with the 2012 clash between Andy Murray and Baghdatis ending at a more gentle 11:02 p.m.
