A Mario Mandzukic hat-trick saw off the tame challenge of Hamburg as Bayern moved a step closer to their third trophy of the season after winning the UEFA Supercup and FIFA World Club Cup already.
Dante and Arjen Robben were also on target in a one-sided game, a 5-0 win at the HSV Arena which could also signal the end of Bert van Marwijk's reign as coach.
The northern Germany side slipped into the bottom two of the Bundesliga off the back of six straight defeats at the weekend while their humbling in the cup further increases the pressure.
Kaiserslautern created the upset of the round with their extra-time victory at Leverkusen.
Mohamadou Idrissou missed a penalty in extra-time for the visitors, but as it looked like the game would be decided by 10 further spot-kicks, Ruben Jenssen scored to seal victory for the 2. Bundesliga side.
They were joined in the last four by Wolfsburg, who won 3-2 at Hoffenheim.
Ricardo Rodriguez scored two penalties for the visitors with Bas Dost also on target for Dieter Hecking's men.
Roberto Firmino scored both of Hoffenheim's goals, but they were unable to find an equaliser, despite playing 10 men with Rodriguez sent off.
Borussia Dortmund were the first side to make it into the semi-finals on Tuesday night thanks to a 1-0 win at Eintracht Frankfurt.