After the drama of Luca Toni's 120th minute equaliser which sealed a 3-3 draw in Getafe in the quarter-finals to put the Germans in the last four, Bayern will now have their work cut out.
French midfielder Franck Ribery put his side ahead with an 18th minute penalty until Brazilian Lucio turned the ball into his own net in the second half.
"It will be difficult next week, but it is still possible," admitted Bayern striker Lukas Podolski. "We don't need to have any fear, because we are the better team. We played a decent game today, but we conceded a stupid goal."
After winning the German Cup in Berlin by beating Borussia Dortmund last weekend - and the League Cup earlier in the season - Bayern are still aiming to lift their third cup this season, but Dick Advocaat's side will give them a stiff test on home turf.
Bayern were without suspended Italian striker Toni, who has scored 10 UEFA Cup goals in the campaign so far including the two crucial efforts in extratime in Getafe which put his side in the semifinals.
It took just 18 minutes for Bayern to go ahead when midfielder Ze Roberto was fouled in the penalty area by St Petersburg's Dutch midfielder Fernando Ricksen and Ribery converted the penalty.
After his first effort was saved, Ribery smashed home the rebound to give his side the lead over the Russian champions who humiliated Bayer Leverkusen 4-1 at home in the quarter-finals.
But the Russians were back on level terms on the hour mark when midfielder Viktor Fayzulin whipped in a cross and Bayern defender Lucio headed the ball past his own goalkeeper Oliver Kahn.
A thigh injury saw Kahn make way for Bayern's reserve goalkeeper Michael Rensing on 66 minutes and his forlorn figure trudging off the pitch summed up the home side's mood. With Kahn set to retire at the end of the season, he faces a race against
time to be fit for Thursday's second leg while striker Miroslav Klose is also struggling after breaking his nose in the game.
"It is too early to know the gravity of Kahn's injury," said Hitzfeld.
Lucio went close on 78 minutes when he unleashed a fierce drive, but Russian goalkeeper Vyacheslav Malafeev tipped the shot over the cross bar.
Having won Bayern the early penalty, Ze Roberto then kept his side in the game when he cleared a shot off the line after the ball trickled through Rensing's legs.
Germany striker Lukas Podolski had a golden chance to snatch the winner in the 90th minute but his shot went just wide of the post. That allowed the Russians to finish the game the stronger leaving Bayern with a huge task in St Petersburg next Thursday.