Mauricio Pochettino's men had drawn four of their five previous league games before second-placed Nice closed to within eight points by beating Nantes
The Premier League's top teams are all in action with the feature attraction being Steven Gerrard's return to Anfield as manager of Aston Villa.
PSG equalised in the second minute of injury time as Kylian Mbappe crossed for fellow substitute Wijnaldum to head home.
Rayan Cherki's 89th-minute strike snatched the points for Lyon, who had lost the lead just three minutes earlier to a Wissam Ben Yedder penalty.
Marseille climbed up a place to fifth, which offers qualification to the new Europa Conference League competition next season.
European football matchday: Chelsea travel to Leeds United; Bayern Munich at Bremen in most-contested fixture
Chelsea are in the fourth Champions League spot, two points ahead of West Ham, who have a game in hand.
European football weekend: Jorge Sampaoli in focus, title races intensify in Spain, Italy, Germany and Seville derby
We take a look at the key matches in European football this weekend.
Ligue 1: Jose Fonte's late header helps Lille draw against Strasbourg; Monaco extend unbeaten run to 12 games
Lille are now two points ahead of second-placed Paris Saint-Germain, although Lyon could move within a point of the pace-setters when they visit Marseille later on Sunday.
Ligue 1: Stefan Jovetic, Kevin Volland score late as Monaco defeat Brest to make it 12 games unbeaten
The win took Monaco to level on points with third-place Lyon.
Lyon were in cruise control with a 3-0 lead courtesy of goals from Lucas Paqueta in the ninth minute, Houssem Aouar after 28 minutes and a penalty from Memphis Depay just before the half-time break.
PSG are second at the season's halfway stage, a point behind the leaders Lyon and ahead on goal difference of third-placed Lille, who triumphed 1-0 at Nimes.
Ligue 1: Lille suffer first defeat of season at Brest, Lyon grab derby bragging rights over St Etienne
Paris Saint-Germain pulled five points clear at the top of the French league after Lille lost 3-2 at Brest on Sunday and surrendered the only remaining unbeaten record.
Ligue 1: Lyon find momentum ahead of Champions League clash against Juventus with win at Metz; Nice draw at home against Brest
Lyon hosts multiple Italian champions Juventus in the first leg of their last-16 Champions League game on Wednesday
Coupe de la Ligue: Mauro Icardi continues goalscoring form as Paris Saint-Germain thrash 10-man Saint Etienne
Argentine Icardi, on loan from Inter Milan, scored either side of the interval with Neymar, a Jessy Moulin own goal and a Kylian Mbappe effort adding to the woes of Les Verts, who were reduced to 10 men when Wesley Fofana was sent off after half an hour
Ligue 1: Nemanja Radonjic strikes late against Brest as Olympique de Marseille narrow gap on leaders PSG
Second-half substitute Radonjic found the top corner a minute after Irvin Cardona had cancelled out Bouna Sarr’s second-half opener to put second-placed Marseille on 28 points from 15 games ahead of PSG’s trip to AS Monaco on Sunday.
Mauro Icardi came off the bench to score a late winner as Paris Saint-Germain extended their Ligue 1 lead to nine points despite another unconvincing performance in a 2-1 victory at Brest on Saturday.