Inter, who got the better of Bayern in last year’s final, made a lightning start at the Allianz Arena, levelling the tie on aggregate after just three minutes when Pandev fed Samuel Eto’o and the Cameroon international coolly slotted home.
Bayern were gifted the equaliser 18 minutes later when Cesar failed to hold onto a long-range effort from Arjen Robben, and Mario Gomez was on hand to chip the ball over the Inter goalkeeper and into the net.
The Germans then went a goal ahead on the night, and two on aggregate, when Robben’s pass was deflected into the path of Thomas Muller and the Germany international produced a clinical finish on the half-hour mark.
Cesar made a smart stop to prevent Franck Ribery extending Bayern’s lead, and Inter were then fortunate to remain in the tie when Andrea Raonicchia’s attempted clearance hit Muller but came back off the post.
Inter hauled themselves within one goal of an away-goals victory just after the hour-mark when Wesley Sneijder curled a low shot past Thomas Kraft, and the crucial strike came late as Eto’o found space in the area and turned provider for Pandev to smash home the winner.