Brandao first scored a late equaliser for Marseille to send the game into extra time after a second-half header by France forward Andre-Pierre Gignac had put Toulouse in front.
The winner came just before the extra time interval with Brandao scoring with a powerful shot.
Marseille, who have never won the League Cup, will meet the winner of the other semi-final between Lorient and holders Girondins Bordeaux on March 27 at the Stade de France.
Lorient and Bordeaux play on February 17.
Marseille created more of the limited chances in the first half but both Argentine midfielder Lucho Gonzalez's long range effort and Senegal striker Mamadou Niang's header went wide.
Both teams played at a higher pace after the break and the home side broke the deadlock thanks to a Gignac header at the far post from an Albin Ebondo cross just before the hour.
Brandao headed home the equaliser from a Hatem Ben Arfa cross four minutes from the end of normal time.
Two French Cup round of 32 games were also played on Wednesday and Ligue 1 strugglers St Etienne needed a penalty shootout to overcome fourth-division Villefranche after a 2-2 draw.
Sochaux also qualified with a 3-0 demolition of Le Mans at home in an all-Ligue 1 tie.
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