Federer, 39, took three hours and 35 minutes to see off the 27-year-old German 7-6, 6-7, 7-6, 7-5 on centre court.
The night session match finished at around 12.45am on Sunday morning on an empty centre court. Organisers have not been able to house spectators due to a government imposed 9pm curfew to stem the spread of the coronavirus pandemic.
During his post-match press conference just before 2am, Federer, who had played only three matches in 16 months after two operations on his knees, hinted that he would analyse his reaction to the match.
During Sunday afternoon, the 20-time Grand Slam champion released a statement through the French Open organisers.
Care
"After over a year of rehabilitation it's important that I listen to my body and make sure I don't push myself too quickly on my road to recovery.
"After discussions with my team, I've decided I will need to pull out of Roland Garros," Federer said.
"I am thrilled to have gotten three matches under my belt. There is no greater feeling than being back on court."
He had been due to face ninth seed Matteo Berrettini on Monday.
Federer had two knee surgeries last year and had played only three matches in 16 months before arriving in Paris.
