Nice climbed to fourth on 29 points after 16-year-old Neal Maupay's stoppage-time goal secured a 3-2 home victory over Evian Thonon Gaillard.
It was the first league goal in six appearances for Maupay who came off the bench in the 86th minute.
Half-time substitute Gignac, who returned on Wednesday after six weeks out with a broken foot, bent a powerful shot into the top corner in the 68th minute to earn Marseille's seventh away victory of the season.
"It is a beautiful story for me," Gignac told reporters after sinking former team Toulouse who played the entire second half with nine men.
"It made it easier for us but they played with a lot of heart. Tonight luck was on our side."
The first Toulouse player to receive a red card was Cheikh M'Bengue when he produced a rough tackle on Morgan Amalfitano in the 28th minute.
Marseille won a penalty 13 minutes later when Franck Tabanou fouled Jordan Ayew but his older brother Andre Ayew's spot-kick was saved by Toulouse's outstanding keeper Ali Ahamada.
Marseille went close to scoring again when Ahamada saved Joey Barton's volley and a powerful effort from Lucas Mendes.
"We began well but then ruined it all," said Toulouse coach Alain Casanova referring to the two red cards.
Casanova's men have only won once in eight league games and occupy 12th spot on 23 points.
Elsewhere, Marco Estrada's spectacular 35-metre volley in the 14th minute set champions Montpellier on the path to a 4-0 home drubbing of Bastia.
Montpellier's fourth win in five games took them up to ninth on 26 points, level with Lille who drew 1-1 at promoted Stade Reims.
