Loic Remy had given the home side an early lead, before Anthony Mounier equalised just before the interval.
However, twelve minutes into the second-half, Brandão turned up to add the winning goal for his side and send the fans into raptures.
After a season of misfiring at Grêmio and Cruzeiro, Brandão has now scored twice in his first four games back in France, suggesting at least a temporary return to form.
Marseille will now meet Lyon in the final.
