Argentina forward Mauro Icardi doubled the lead before Spain midfielder Pablo Sarabia scored from 20 yards.
PSG are one point behind leaders Lyon, who were held 2-2 at Rennes.
Pochettino’s first game in charge had ended in a 1-1 draw away to Saint-Etienne on Wednesday.
PSG, who were again without Brazil forward Neymar because of an ankle injury, lived dangerously before scoring two late goals to win for the first time since the former Tottenham and Southampton boss took charge on 2 January.
With third-placed Lille winning 1-0 away to Nimes, there is one point separating the top three in Ligue 1.