Pepe got a brace and it was his second goal that won the Stade Pierre-Mauroy outfit the maximum points.
The visitors got off to a fine start in the Stadium Municipal after the Cote d'Ivoire international opened the scoring in the fifth minute.
However, the lead was shortlived as Corentin Jean equalised four minutes later before Christopher Jullien added another goal for the Toulouse outfit before the break.
Bissouma started the turnaround for Lille with his leveller in the 80th minute - his second goal in 22 league matches this season.
Two minutes later, Pepe sparked celebration in the away stands with his second goal that stood as the winning effort for the Dogues.
The forward has now scored 13 goals in 29 league appearances this campaign.
South Africa's Lebo Mothiba was action for 72 minutes before being substituted for Anwar El Ghazi, while on-loan Bournemouth star Max Gradel played for 79 minutes as Toulouse suffered their second consecutive loss in the league.
The win powered Lille out of relegation zone with 35 points from 36 games. They welcome Dijon for their next league game on May 12.