PSG, who play at the Emirates Stadium on Wednesday with top spot in Group A at stake, are second in Ligue 1 with 29 points from 13 games, behind leaders Monaco on goal difference.
Third-placed Nice, who also have 29 points, will reclaim the lead if they avoid defeat at St Etienne on Sunday.
Angel Di Maria netted the first goal, his first in Ligue 1 this season, in the opening half before limping off with a suspected thigh injury. Jese wrapped up the win with a late penalty.
Di Maria's Argentine compatriot Javier Pastore, who came on as a late substitute for his first appearance since suffering a calf injury in September, sustained a knee problem in stoppage time.
PSG are already without influential midfielder Adrien Rabiot for the Arsenal game after the France international was injured with the national team earlier this week.
Di Maria slotted home after being set up by forward Jean-Kevin Augustin who started up front as coach Unai Emery rested Uruguay striker Edinson Cavani.
Keeper Kevin Trapp, standing in for the injured Alphonse Areola, then denied Guillaume Gillet from point-blank range as Nantes threatened.
Di Maria limped off 10 minutes before the interval and was replaced by Hatem Ben Arfa.
"We took him off as a precaution, I hope he will be fine for Wednesday," said Emery.
Nine minutes into the second half Blaise Matuidi fired a fierce shot against the post.
Second-half substitute Jese then converted a penalty in the last minute before Pastore was hurt in the closing stages.
"I hope it is a minor injury. We will know more when he has seen the doctor," said Emery.
(Reporting by Julien Pretot; Editing by Neville Dalton)
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