The Serbian top seed defeated Stefanos Tsitsipas 6-3, 7-6 (7/3) but only after aggravating the right knee injury that required surgery in June.
Djokovic needed on-court treatment after slipping on the baseline of Court Philippe Chatrier.
He fell 0-4 and then 2-5 down in the second set but battled back to save three set points in the ninth game.
The 24-time Grand Slam title winner, still looking for a first Olympic gold medal, then raced through the tie-break to record his 12th win in 14 meetings against the Greek.
"I will have to check with my medical team," said Djokovic when asked about his fitness issues.
"It's good that I managed to get it done in straight sets and finish the match. But I also finished my fourth-round match at the French Open and then discovered that I had torn my meniscus.
"I need to see what happens now. I don't know what to say. It's day by day. I hope I can be physically fit for tomorrow."
Djokovic will face Italy's Lorenzo Musetti on Friday for a place in the gold medal match.
