The Portuguese side, trailing 1-0 from the first leg, gave themselves hope when Raul Jimenez headed them in front in the return tie at home.
But Arturo Vidal thumped in a shot and Thomas Muller guided in a close-range effort to put the Germans in control.
Talisca curled in a free-kick for Benfica after Javi Martinez escaped a red card before Bayern progressed.
Bayern boss Pep Guardiola will join Manchester City this summer and the two clubs could meet in the last four when the draw is made on Friday.
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