Sinner's clash with Mackenzie McDonald did not start until after midnight and his 6-7(6) 7-5 6-1 win ended at 2:37 a.m., with his third-round tie against Alex de Minaur scheduled for Thursday afternoon, drawing criticism for the organisers.
"I am sorry to announce that I am withdrawing from today's match in Bercy," Sinner said on social media platform X.
"I finished the match when it was almost three in the morning and didn't go to bed until a few hours later. I had less than 12 hours rest to prepare for the next game."
Sinner has already qualified for the ATP Finals in Turin which begin on November 12th. Australian De Minaur will now face Andrey Rublev in the quarter-finals after the walkover.
"I have to make the right decision for my health and my body," Sinner added.
"The weeks ahead with the ATP Finals at home and the Davis Cup will be very important, now I focus on preparing for these important events. See you in Turin."
After the late-night win over McDonald, Sinner had already hinted at his withdrawal, saying he did not know yet if he would play the next round and would decide when he woke up.
Before Sinner's withdrawal was announced Norwegian Casper Ruud defended the Italian and criticised the ATP.
"Bravo ATP, way to help one of the best players in the world recover and be as ready as possible when he finished his previous match at 2:37 a.m. this morning, 14.5 hours to recover... what a joke," Ruud wrote on X, formerly known as Twitter.
Late finishes are commonplace at other tournaments, including the US and Australian Opens, with Andy Murray describing his 4:05 a.m. finish in a match against Thanasi Kokkinakis in Australia this year as a "farce".
Elena Rybakina said she felt "destroyed" by the Montreal schedule after her quarter-final ended at 3 a.m. in August.
Despite the complaints, the US Open has no plans to change its schedule.
"We looked at starting the evening session earlier, instead of 7 p.m. start at 6 p.m., but it's not really a possibility because it's hard for New Yorkers to get here even at 7 p.m.," tournament director Stacey Allaster said.