France international Mbappe slotted in an early opener after initially missing his volley.
He then doubled the lead midway through the first half when he was superbly put through by Lionel Messi and produced a clinical finish.
Sada Thioub scored a late consolation for the hosts.
The victory means PSG move onto 75 points and lead Marseille - who play Lyon on Sunday - by 11 points with six games remaining.
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