Goals for the Germany and Netherlands internationals left the Bavarians in pole position to advance to face the winner of the tie between APOEL and Real Madrid
Franck Ribery's return to the Stade Velodrome was not exactly a comfortable one, but the visitors overcame stiff resistance as they secured a two-goal advantage ahead of the return leg in Munich.
One minute before half-time, Mario Gomez found the net under controversial circumstances after a suspected hand-ball at the other end. The goal counted nonetheless, and OM were forced to try to overturn the deficit. However, Arjen Robben scored a crucial second goal on 69 minutes, leaving the hosts with a mountain to climb.
Chances were few and far between in what was a physical opening half. Though cautious in their approach, the hosts were first to pose a threat on goal and were unfortunate not to take the lead on seven minutes. Following a corner-kick, Rod Fanni's header was tipped wide by Manuel Neuer. Loic Remy was first to the rebound, but blasted into the side-netting.
After a tough start, Bayern gathered some fluency in midfield and carved out a couple openings inside the Marseille penalty area. However, Robben slipped before seeing his window to shoot close, and Thomas Muller's low cross found no team-mate in the centre before rolling out of play.
Marseille recovered, and shortly before half-time, a botched clearance from Jerome Boateng saw the ball fall to Remy. The striker was quick to shoot from the edge of the penalty area, but Neuer pounced to make a save.
Bayern as well would benefit from a mistake shortly thereafter, but the Germans took their chance as Gomez fired in off Elinton Andrade's hands. Seconds before, Mathieu Valbuena had kicked the ball off Philipp Lahm's hand, but play continued as Robben slipped in Gomez, whose finish appeared to be covered by the goalkeeper before it deflected into the net.
After the break, Marseille had an encouraging start, with Valbuena nodding over the bar from Remy's cross. Andre Ayew headed on goal in the 56th minute, but Neuer had little trouble in making a stop. Shortly before the hour mark, Remy muscled Boateng off the ball, but Neuer was quick off his line and blocked the forward's attempt.
The balance swung in the visitors' favour around the hour mark, however. Andrade did very well to deny Gomez, but with 21 minutes left, Robben made it 2-0, handing the visitors a big advantage heading into the second leg. The Dutchman played a one-two with Muller, and curled his finish inside the left post.
The most significant action late in the game was a booking for Bayern substitute Bastian Schweinsteiger, who will miss the second leg through suspension. In addition, OM's Alou Diarra will sit out, having been booked earlier in Wednesday's match.
The result sees Bayern take a commanding lead into the second leg, which will be played on April 3. The winner of the two-legged tie will face either APOEL or Real Madrid in the semi-finals.