Messi tested positive for COVID-19 while back home in Argentina and subsequently missed PSG’s 4-0 victory over Vannes in the Coupe de France last Tuesday (AEDT).
The seven-time Ballon d'Or winner returned a negative test on Thursday (AEDT) and was set to be available to face Lyon.
But the Ligue 1 leader confirmed on Sunday (AEDT) that the 34-year-old will "continue his post-COVID individual recovery protocol for the next few days".
PSG also revealed that Angel Di Maria, Julian Draxler, Danilo Pereira, Layvin Kurzawa and Gianluigi Donnarumma remain in isolation after recently returning positive tests.
Meanwhile, Neymar is resuming his rehabilitation and is scheduled to return to training in three weeks' time.
Head coach Mauricio Pochettino acknowledged that PSG must adapt in the absence of players, but insisted that every team is in the same boat.
During his pre-match press conference, he said: "All teams have absent players; so do we. We have to adapt to everyday life. Sometimes, we have to change our plans.
"It's the same every game, we always have to make choices. We have to put the players in the best conditions."
On the prospect of facing Peter Bosz's Lyon side, he added: "They are one of the best teams in France.
"There is a very great coach. In the end, they will be fighting for the first places.
"It will be difficult, but we are optimistic."