Messi played the full 90 minutes of their 2-1 defeat to Marseille in the French Cup on Wednesday.
However, he later felt pain in his hamstring.
Messi is expected to miss PSG’s trip to AS Monaco in Ligue 1 on Saturday, three days before the Bayern fixture.
Messi has scored 15 goals in 25 games in all competitions for PSG this season.
The French champions are already without forward Kylian Mbappe for the game after he picked up a thigh injury last week.
The second leg will be held in Munich on March 8.