Partizan had led through Mladen Krstajic's 24th minute header, but two goals in nine minutes from Pantxi Sirieix after the half-hour mark turned the game on its head against the run of play.
Toulouse then added a third through Antoine Devaux before substitute Cordova Cleo got one back for the hosts.
The game took place in the shadow of ugly scenes beforehand that left two French fans and one Serbian in serious condition in hospital.
Chances were few and far between in the early stages, with the first effort on goal coming in the 19th minute when Xavier Pentecote tried his luck from long range but could not beat Darko Bozovic in the Partizan goal.
Radosav Petrovic went closer for Partizan moments later when his effort brought a fine save from Yohann Pele, who tipped the ball around the post.
But from the resulting corner the hosts went ahead as Marko Lomic's cross picked out Krstajic who sent his header low and left into the net.
Toulouse responded eight minutes later when Pentecote crossed for Sirieix to finish from close range.
But Partizan remained on top with Srdan Knezevic seeing his effort blocked by Pele, who then had to make another good save to deny Krstajic with a follow-up.
It was against the run of play that Toulouse took the lead seven minutes before the break as Sirieix got his second, firing in from the edge of the area after good work from Etienne Capoue down the left.
Toulouse capitalised on their good fortune as they built a two-goal advantage soon after half-time with Sirieix turning provider to set up Devaux for the finish.
Lamine Diarra did his best to get Partizan back in the game, seeing his first shot punched clear by Pele before a second was charged down by Cheikh M'Bengue.
Instead, Diarra had to settle for an assist, with his cross turned in by Cleo with 25 minutes to go.
They were back within touching distance, but Nemanja Tomic could not draw Partizan level as his shot from the edge of the area flashed wide.
At the other end, Andre Pierre Gignac brought a good save out of Bozovic, but Toulouse would be happy to shut the game down and collect the three points.