Messi had limped out during Friday's 2-1 win over Lille in Ligue 1 and was not in Tuesday's 21-member squad for their Champions League Group A match in Germany.
Messi missed training in preparation for the match against Lille and was replaced by MauroIcardi. After moving to PSG this summer, the former Barcelona forward has not scored a Ligue 1 goal.
Mbappe's teammate, however, had to miss the Lille match due to an infection and was part of PSG's Champions League squad.
With seven points from three games, the French club is leading Group A. Manchester City is second with six. After losing all three of their games, Club Brugge is on four points and Leipzig has yet to score a point.