كتب : Hatem Maher
Two goals from Pavel Pogrebnyak and Konstantin Zyrianov in the first half helped Zenit firmly control the game.
Viktor Fayzulin added the third shortly after restart before Pogrebnyak compounded Bayern's misery in the 73rd minute.
Bayern were eliminated after a 5-1 aggregate defeat as the first-leg ended in a 1-1 draw at Allianz Arena.
The Bavarian giants won the German Cup and are on the brink of clinching the Bundesliga title.
Zenit will face either Fiorentina or Rangers in the final at the City of Manchester stadium on May 14.