The France forward was substituted in the closing moments with a heavily strapped thigh, casting doubts on his fitness ahead of PSG's Champions League semi-final first leg at home to Manchester City on Wednesday.
"We hope it's not too serious," PSG coach Mauricio Pochettino told reporters. "Kylian was calm when he was replaced but even a simple knock is always painful."
Against the run of play, Metz scored their first goal in four league matches to equalise at the start of the second half as right back Fabien Centonze headed home a dipping cross by attacking midfielder Farid Boulaya.
PSG reclaimed the lead in the 58th minute when Mbappe capitalised on a misplaced Centonze pass, before scoring his 25th league goal of the season with a deflected effort from outside the box.
Mauro Icardi's cheeky 'Panenka' penalty sealed the result with two minutes remaining as PSG moved two points clear of second-placed Lille, who have a game in hand against Olympique Lyonnais on Sunday.
The result rounded off a successful week for PSG as they remained on course for an historic treble of domestic league and cup and European Cup this season, having defeated Angers to reach the French Cup semi-finals in midweek.
"We are on the right track, there is still a month of competitive football to go, we are still in the cup, in the league and in the Champions League," Pochettino added.
"We are battling to win all three; we want to accomplish what we want to do at the end of the season."