Unlike Angel Di Maria, Julian Draxler and Kylian Mbappe, Cavani started at Parc des Princes but he only lasted 45 minutes before hobbling off.
His departure came moments after he converted a first-half penalty after Nicolas de Preville's clumsy challenge on the marauding Thomas Meunier.
The loss of Cavani seemed to affect PSG after the restart as it struggled to re-assert its dominance, Gianluigi Buffon needing to make a number of saves to ensure the lead at the top of the Ligue 1 grew to 13 points.
Thomas Tuchel made seven changes from the side beaten at Lyon last weekend but it did not affect its rhythm, and Thiago Silva should have put it ahead early on but his shot was cleared off the line by Pablo.
While Silva was unlucky, Cavani was wasteful when played in by Marco Verratti, the Uruguay international controlling the chipped pass well before hooking his left-foot shot well wide.
Eric Maxim Choupo-Moting was denied at point-blank range by Benoit Costil as PSG began to apply pressure, the forward unable to convert from Christopher Nkunku's run.
With half-time looming PSG finally took the lead, Meunier fouled by De Preville and Cavani making no mistake from the spot.
It was Cavani's final action as the striker limped off with a muscle injury, Mbappe coming off the bench to replace him at the start of the second period.
PSG was lucky to still be ahead just before the hour when Younousse Sankhare created space for Francois Kamano, but the forward ballooned over from 18 yards much to the relief of the home defence.
Buffon then made a superb save to deny Kamano's next effort and PSG withstood some late pressure before its return to winning ways in the league was confirmed.
While the win extends PSG's lead at the top of Ligue 1, it may come to rue starting Cavani if he misses the midweek trip to Old Trafford. Tuchel will hope removing him at the break ensured he will be fit to feature as it looks to keep European dreams alive.