Brandao gives Marseille third straight League Cup
Marseille win the 2012 edition
The Brazilian beat Hugo Lloris with a low shot in the 105th minute to settle a low-quality encounter and end a desperate run of form that had seen Marseille go 12 games without victory in all competitions.
Having slumped to ninth in Ligue 1 and been swept out of the Champions League by Bayern Munich, victory over OL means Didier Deschamps' side can at least look forward to Europa League football next season.
Lyon's four-year trophy drought continues, but they will hope for better luck when they return to Stade de France to face third-tier Quevilly in the French Cup final in two weeks' time.
There was an early scare for Marseille when Lisandro Lopez headed wide from an offside position but the initial exchanges were scrappy, typified by a miscued cross by Kim Kallstrom that sailed yards over the OM crossbar.
Lyon played narrowly, and invited Marseille to attack them, but the holders' forward forays lacked penetration and at times the game's tempo brought to mind an exhibition match.
Half-time arrived without either goalkeeping having been tested, although Anthony Reveillere had to be alert to thwart Loic Remy as he strode into the Lyon area in the 39th minute.
The capacity crowd had to wait until the hour for a shot on target, but Bafetimbi Gomis' header was straight at Marseille goalkeeper Steve Mandanda and again, the assistant referee's flag was raised.
It stung Marseille into action and in the 65th minute Morgan Amalfitano came close to making the breakthrough when his header from Mathieu Valbuena's left-wing cross was touched onto the post by Lloris.
The stadium came to life but the excitement was to prove short-lived as the play quickly regained the disjointed, soporific quality that had characterised the first period.
Gomis planted a header over the bar from a left-wing corner in the 84th minute and it was to prove the last action of note before extra time.
Valbuena shot straight at Lloris mid-way through the first extra period, while Gomis flashed a left-foot effort across the face of goal at the other end.
Jimmy Briand then blazed over the bar after being set free in the OM box and moments later Brandao claimed the winner, just nine minutes after coming on for Remy.
The Brazilian stole in front of Samuel Umtiti to claim Benoit Cheyrou's centre and then held his nerve to fire the ball between Lloris' legs from six yards and haul his side out of their springtime gloom.
It could have been worse for Lyon, but Lloris clawed away a goal-bound Andre Ayew header shortly after the half-time interval in extra time.
A second yellow card for centre-back Dejan Lovren, apparently for dissent, meant that Remi Garde's side finished the game with 10 men, their misery complete.