The Argentina international sustained the problem during PSG's late 2-1 win against Lyon on Monday (AEST) as it made it six wins from six to begin the new league campaign.
Messi made his home debut in that match but was substituted with the scores level, meaning he has yet to score in three appearances since joining from Barcelona last month.
PSG will not have Messi in its squad to face Metz at Stade Saint-Symphorien, with that game coming six days before a UEFA Champions League trip to Guardiola's Manchester City.
The French giant confirmed the injury blow in an injury update posted on its official website.
"Messi, following the blow received on his left knee, underwent an MRI which confirms the signs of bone contusion," the update read. "A new test will be carried out in 48 hours."
PSG also confirmed that Marco Verratti returned to training on Tuesday, while Sergio Ramos – yet to feature since joining from Real Madrid – is continuing to train individually.
Pochettino's decision to bring on Achraf Hakimi for Messi with his side chasing a goal against Lyon dominated all the talk after last weekend's contest.
Messi was involved in six shots (four attempts, two chances created) – only Kylian Mbappe against Clermont (seven) has managed better in a league game for PSG this term.
Pochettino insisted there were "no issues" with Messi when speaking after the game and has once again defended his decision to bring off the six-time Ballon d'Or winner.
"I understand the situation and accept it as it is," Pochettino said at a news conference on Wednesday (AEST) ahead of the clash with Metz.
"The priority is always the players and their well-being. We thought the best decision was to take him off. But of course, all champions want to be on the pitch all the time."
Asked to elaborate on Messi's injury, Pochettino said: "The club have already communicated that. During the match we saw he was checking his knee after being struck.
"When we saw that we made a decision. We were happy with his performance and I am happy with his commitment. He didn't score but was otherwise very good."
Mbappe had a quiet game against Lyon before assisting Mauro Icardi's late winner as he touched the ball just five times in the opposition box and failed to get a shot on target.
The Frenchman spearheaded a 4-2-3-1 formation that also included Messi, Neymar and Angel Di Maria in attack and Pochettino insists it will take time for system to work.
"We have to create these connections in training over time, not just in matches," Pochettino said. "We used a 4-2-3-1 against Lyon and that's not the same as we've used before.
"That's why I was happy with the team's performance. We were also organised in defence and recovered balls high up the pitch.
"Leo, Neymar and Di Maria know each other well and have already built a connection. Now we have to integrate Kylian into the side and that will take a while."
Mbappe is expected to start against Metz on Thursday (AEST), an opponent he has either scored or assisted against in all five previous Ligue 1 encounters.
PSG also has a great record against Metz, having defeated it in 10 successive league fixtures in a run stretching back to August 2007.