The Ukrainian forward, on loan from Liverpool, scored either side of half-time to put Hertha top of the league and knock Hoffenheim into second spot following their shock 4-1 hammering by Bayer Leverkusen on Friday.
Voronin opened the scoring mid-way through the first-half, but Bayern equalised through Germany striker Miroslav Klose after the break only for the Ukrainian to score his second with time running out to put his side top.
"Beating Bayern is obviously a bit special," said Voronin after his two superb strikes at Berlin's Olympic Stadium. "We're top of the league, and the whole city and club will be overjoyed. We were disciplined, we kept it tight, and we gave them very few chances."
Voronin said the first-half injury to Bayern's Luca Toni, who was forced off with an Achilles tendon injury, helped Hertha's cause as Munich lost their Italian World Cup-winning striker who was the league's top-scorer last season.
"We were lucky too when Luca Toni had to go off. But Bayern weren't as good as we'd been expecting," he said.
And Hertha's Swiss coach Lucien Favre said it was his finest hour since he took over in July 2007.
“I have to say this is the best day I've had since coming to Hertha," he said. "It's just fantastic. I'm truly delighted. We were a unit out on the field today. The 2-1 scoreline isn't undeserved."
But Bayern boss Jurgen Klinsmann was fuming after his side missed a golden chance to go top of the table for the first time this season as they slumped to their second league defeat in their last three games.
"We're very disappointed, and angry about missing out on first place," said Klinsmann. "The lads are sitting in the dressing room and saying to themselves: 'that's unbelievable', but that's football,” he said. "I still think we'll take first place sooner or later. We'll sit down now and analyse the match,” he said. "I think the team recognises we lacked the necessary spark to score the decisive goal ourselves and avoid inviting our opponents to hit us on the break."
The result leaves Hertha top of the table by a single point over second-placed Hoffenheim, while defending champions Bayern drop to third.