The seven-time Ballon d'Or winner tested positive for the virus while in his native Argentina last week but flew back to Paris on Wednesday.
He missed PSG's 4-0 French Cup win against Vannes on Monday.
The club did not say if Messi would be available for their first Ligue 1 match since the winter break, at Lyon on Sunday.
"The test carried out by Leo Messi was negative for Covid-19. He has arrived in Paris and he will resume with the group in the coming days," PSG said in a statement.
Messi has endured a difficult start to life in the French capital since an emotional exit from Barcelona last summer.
He has scored only one goal in 11 league appearances for PSG, although he has netted five times in the Champions League.
The French capital giants also said that full-back Layvin Kurzawa had tested positive for Covid on Wednesday and was in self-isolation.
Goalkeeper Gianluigi Donnarumma, defender Juan Bernat, back-up keeper Sergio Rico, midfielder Danilo Pereira and teenager Nathan Bitumazala have all also returned positive Covid test results in the past week.
