The French club won the Round of 16 first leg 1-0 at home and although they went down 2-1 at the San Siro tonight, Brandao's injury-time goal was enough to send them through to the final eight despite it being a 2-2 aggregate.
Claudio Ranieri's Inter finally got the goal they needed to get back into the tie when Diego Milito pounced on a loose ball in the 75th minute. The Argentine was able to slot home from the six-yard box after substitute Giampaolo Pazzini's initial effort was blocked but it feel straight to Milito who made it 1-0 on the night.
Just as it looked like the tie would head to extra-time, Marseille substitute Brandao popped up to control keeper Steve Mandanda's long ball on the edge of the area before firing home past Julio Cesar to make it 1-1 on the night and 2-1 on aggregate.
A few minutes later, Inter were given a lifeline when Pazzini was brought down in the area by Mandanda, who had received his second caution, with Marseille number two Gennaro Bracigliano stepping straight into the firing line but being unable to keep out the spot kick.
Although the converted penalty gave Inter the second leg win, it was Didier Deschamps and his Marseille bench who were celebrating as they move into the quarter-final phase for the first time.
UEFA Champions League Round of 16 - second leg
San Siro, Milan - 50,000
Red cards:MAR - Steve Mandanda 90+3'