Between them Brazilian Grafite and Bosnian Dzeko have now scored 35 goals in 41 games this season as Wolfsburg defended their unbeaten home record and went top after Hertha Berlin lost at home to Dortmund.
For Wolfsburg's ex-Bayern coach Felix Magath, it was sweet revenge against the club that sacked him in February 2007 as his side went top of the table for the first time this season while Bayern dropped to fourth.
"That was an unusual game for us, because it is not every day you get such a result against Bayern Munich," said Magath, who has previously insisted his side are not good enough to win the Bundesliga.
"In the first half, Bayern were better, but we got a lot stronger after the break and played some heady football. But our goal remains to finish the season in the top five."
Every single Bayern player refused to be interviewed live on television after the game and coach Jürgen Klinsmann admitted the result was devastating, especially ahead of Wednesday's daunting Champions League trip to Barcelona.
"Nothing about the game was pleasing," said the glum ex-Germany boss. "To fly back to Munich after such a result is not pleasant. We put in a good first-half, but deserve all the criticism we will get for the second half."
"This defeat hurts - especially before our Champions League quarter-final at Barcelona on Wednesday. Wolfsburg now stand where we want to be."
With the scores level at 1-1 after an hour, Dzeko struck twice in two minutes - showing top-class finishing for his second goal. It started when Wolfsburg goalkeeper Diego Benaglio rolled a pass to play-maker Zvjezdan Misimovic, which the Bosnia midfielder flicked on to compatriot Dzeko, who placed his shot with pin-point accuracy.
Not to be outdone, Grafite underlined his place as the league's top scorer as he struck twice in three minutes to seal Bayern's humiliation.
For his second on 77 minutes, he beat three defenders and goalkeeper Michael Rensing before back-heeling into an empty net to leave Bayern red-faced.
"We need to look forward and turn the corner as quickly as possible," said Klinsmann, "We have to swallow this bitter pill for now. Obviously, we'll discuss the mistakes we made, but we'll turn our focus to Barcelona immediately.”
"We're all professionals and we have to pick ourselves up, even after we've taken a beating. We'll get back on our feet, and we'll play much better in Barcelona."
Klinsmann told reporters he made his side watch the sobering loss on Saturday night to learn from their mistakes.