Didier Deschamps had called on his side to bounce back after last week's defeat to Brest ended an unbeaten run of 15 matches in all competitions.
But his side were unable to respond with a win as Abdennour headed the winner for the visitors after 67 minutes.
The win moved Toulouse above their opponents into seventh in the table.
Toulouse created the first chance when Etienne Didot set up Etienne Capoue, but he shot wide from close range.
Jordan Ayew had Marseille's first chance but after dribbling past Capoue his effort was blocked by goalkeeper Ali Ahamada.
Toulouse went close when Didot's free-kick found Capoue but his off-target shot was headed into the side netting by Abdennour to leave the game goalless at half-time.
Steve Mandanda kept out a Didot shot after 66 minutes but a minute later he could do nothing as Didot's cross was headed in by Abdennour.
The home side were denied with 18 minutes remaining as Brandao flicked the ball towards Morgan Amalfitano, but his first-time shot was blocked by Ahamada.
Emmanuel Riviere could have extended Toulouse's lead with 15 minutes remaining but was just off target when he noticed Mandanda was off his line and cleared the bar with his attempted chip.
Marseille failed to threaten in the remaining minutes and they left the field to the jeers of their fans at the final whistle.