Messi did not look happy as he was brought off and sat on the bench but after picking up a knock, scans have revealed that he has a bone contusion in his left knee, the club confirmed.
There will be another update on the injury in the coming 48 hours, and so PSG will have to face Metz without Messi, who is still without a goal for his new side.
He came close to breaking his duck against Lyon, hitting the crossbar from a free kick and spurning a number of good opportunities. Neymar and Mauro Icardi managed to find the goals to seal the win for PSG.
While Messi has been sidelined again, Marco Verratti has returned to first team training, while Sergio Ramos is continuing his road to recovery after joining from Real Madrid this summer.
Despite looking shaky since the international break, PSG have won all six of their opening Ligue 1 games this season as they look to claw the French title back from Lille.
After facing Metz on Wednesday, they host Montpellier on Saturday before taking on Manchester City in a mammoth Champions League fixture at Parc des Princes.
PSG stumbld to a1-1 draw with Club Brugge in their opening group stage fixture last week, and will be looking to avenge their semi-final defeat to City last season.