Troyes captain Florian Tardieu converted a controversial penalty in the 43rd minute after Lille winger Edon Zhegrova was deemed to have tripped Tristan Dingome.
Lille was reduced to ten men in the 50th when Portugal midfielder Renato Sanches received two yellow cards in quick succession for dissent. Sanches seemed to question the referee's eyesight by putting his hands around his eyes to mimic binoculars.
Troyes striker Ike Ugbo doubled the lead in the 55th by firing a spot kick into the roof of the net after Lille centerback Sven Botman brought him down.
Lille lost another player in the 68th when Turkey forward Burak Yilmaz tackled Tardieu from behind.
Tardieu sealed the win with a third penalty in the 86th after Lille midfielder Benjamin Andre made a poor challenge on substitute Yasser Larouci.
Troyes inched closer to securing safety by moving five points clear of the relegation zone just a year after gaining promotion.
Lille is six points off a Europa Conference League playoff spot with just three rounds left. Strikers Yilmaz and Jonathan David led Lille to the league title last year but have been misfiring this season. Yilmaz and David have scored only one goal each in all competitions this year.
The 35th round ends later Sunday with Marseille vs. Lyon, Monaco vs. Angers, Bordeaux vs. Nice, Montpellier vs. Metz, Brest vs. Clermont, and Lorient vs. Reims.
On Saturday, Rennes beat Saint-Etienne 2-0 to pull within three points of second-place Marseille while ten-man Lens rallied to draw with Nantes 2-2.
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