The defeat on Thursday, May 1, in Petrovsky Stadium crushed Bayern's hopes of scooping a hat-trick this season.
The club has already raised the German Cup and is firmly on course to win the German league title.
Zenit, who also kicked Bundesliga side Bayer Leverkusen out of European competition, looked the stronger side throughout the match.
Their attacking display against the former four-time European champions even impressed Bayern coach Ottmar Hitzfeld, who tipped to win the Cup.
"Any team that beats Bayern 4-0 must be the favorites," he said.
Historic defeat for Bayern
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Bayern Back to Winning Ways as Bundesliga Resumes ... and white case: Zenit looked superior throughout the game Bayern were last beaten 4-0 in European competition 31 years ago when they lost to Eintracht Frankfurt in the last 16 of the UEFA Cup. There was a similar heavy defeat in the 1991/92 competition when they were beaten 6-2 by B1903 Copehnagen in a second-round UEFA Cup tie.
The home side got off to a shaky start when Roman Shirokov had to clear off the line from Miroslav Klose in the second minute, but two minutes later the Russians found themselves in front.
After a foul by Lucio outside the area, Pavel Pogrebnyak hammered home the ball with his left foot, wrong footing Oliver Kahn in goal.
In the 39th minute, Konstanin Zyrianov made it 2-0 to the Russian side. Viktor Fayzulin all but ended Bayern's hopes with a header in the 54th to make it 3-0.
The goalkeeper was again left standing in the 73rd when Dominguez skipped past Philipp Lahm on the right and found Pogrebynak who side-footed the ball into the net from just inside the area to notch up his second goal of the match.
"It was a catastrophic performance," said Hitzfeld, who is moving to coach the Swiss national side next season. "We really had the stuffing knocked out of us."
The defeat was also a sorry European farewell for 38-year-old goalkeeper Oliver Kahn who is retiring at the end of the season. He, however, put a brave face on it.
"It's better to get knocked out like that rather than on penalties, or in a close game," he said.
It is the first time Zenit, coached by Dutchman Dick Advocaat, have reached a major European final.
"It was unbelievable how we played," Advocaat said. "The most important thing is that we didn't give them much room. We had a lot of respect for Bayern. They are a very good team but today was our day."
Bayern Munich cite exhaustion
Bildunterschrift: Großansicht des Bildes mit der Bildunterschrift: It was a sad match for Oliver Kahn, who said, "Sometimes you just want it to end." Bayern chairman Karl-Heinz Rummenigge said the players were "disappointed," but could end the season with their heads held high after "winning two titles" -- the German Cup and almost certainly the Bundesliga.
"We have to recognize that Zenit played a super game," he said. "Let's not forget that the Russian championship has just started and they are fit and fresh, while our team is now really on its last legs."
(Deutsche Welle)
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