Earlier on Sunday, Bordeaux edged in-form Monaco 2-1 at home to briefly climb into third and Saint-Etienne drew 0-0 at home against Montpellier.
In Toulouse, the home team were reduced to 10 men when right back Steven Moreira drove his studs into Bouna Sarr’s knee and received a red card after a video review.
Marseille dominated a scruffy match but struggled to break down Toulouse. The home team defended in depth and even had a chance to take the lead in the 70th minute but goalkeeper Steve Mandanda saved Ibrahim Sangare’s header with his foot.
Marseille responded with a decisive moment of inspiration in the 76th minute.
Dimitri Payet drew defenders then threaded a clever reverse pass to the darting Dario Benedetto who danced past Baptiste Reynet and coolly slid the ball into the goal.
Three minutes later, Toulouse presented Marseille with a second. Left-back Issiaga Sylla drove a clearance into Valere Germain. The ball bounced to Nemanja Radonjic, who advanced into the penalty area and curled a shot into the net.
“We played a good game and the victory is deserved,” said Marseille coach Andre Villas-Boas.
Toulouse “closed up the game after the red card,” said Villas-Boas. “Don’t forget Mandanda’s decisive save before we opened the scoring. We knew that the first goal would be very important.
“We keep our second place and we have to keep going like this.”
Marseille climbed to 25 points from 14 matches, eight behind leaders Paris Saint-Germain but one ahead of Angers. Bordeaux and Saint-Etienne are fourth and fifth on 22. Toulouse remain second from bottom.
Depleted Bordeaux, already deprived of defenders Mexer and Vukasin Jovanovic who were both suspended, midfielder Youssef Ait Bennasser, who could not play because he is on-loan from Monaco, lost centre-back Laurent Koscielny to injury on Sunday morning and winger Jimmy Briand during the warm-up.
Monaco, who had climbed away from the relegation zone with three victories in their previous four league games, took the lead against Bordeaux with a goal by Islam Slimani on 15 minutes.
After that, even though the hosts’ fans fell silent in the first half as part of a protest against their owners, the visitors failed to exploit the makeshift home defence.
Instead, Brazilian Pablo levelled with a powerful header from a corner after 29 minutes.
In the 67th minute, Slimani handled while standing in the wall at a free kick, conceding a penalty and incurring his second yellow card.
Nicolas de Preville converted the spot-kick to give Bordeaux victory.
“There were a lot of players from the starting XI who were not here,” Bordeaux midfielder Aurelien Tchouameni said.
“This shows the strength of character of our team. Some of them didn’t have much playing time this season. They stood up.”
Later on Sunday, Saint-Etienne drew 0-0 at home against Montpellier as the sides managed just two shots on target.