PSG got off to a great start at the Parc des Princes on Sunday and led 2-0 after 14 minutes thanks to goals from Ousmane Dembélé, and Vitinha from the penalty spot.
The visitors gradually got into the game and played with more verve as Georges Mikautadze pulled one back for Lyon before the interval.
Referee Benoît Bastien stopped play in the 53rd minute after the homophobic chants were heard.
PSG captain Achraf Hakimi approached fans standing in the Auteuil stand behind one of the goals and asked them to stop.
A message reminding fans that discriminatory chants were forbidden was then displayed on the stadium's giant screens before play resumed.
PSG was in control in the second half and Gonzalo Ramos sealed the win in the 88th with an agile finish from close range.
In other games Brest scored a 4-1 win over Nantes with substitute Abdallah Sima scoring twice after Kamory Doumbia and Brendan Chardonnet gave them a 2-0 half-time lead.
Meanwhile Nice twice failed to hold their lead in a 2-2 draw at struggling Montpellier, Rennes beat Angers 2-0 and Strasbourg won 3-0 at Le Havre.
Nice remained in sixth place, six points behind Marseille and Monaco.
Last-place Montpellier would have regrets, too, after missing several chances in the last 10 minutes.
It was a lively contest at the Stade de La Mosson, with the teams mustering a combined total of 38 scoring attempts.
