Petric tapped in from close range in the 72nd minute after being teed up by former Bayern midfielder Ze Roberto.
Undefeated Hamburg lead with 17 points from seven matches. Bayer Leverkusen, who had briefly taken over at the top after winning an earlier match 1-0 against Cologne, are behind them on goal difference.
Schalke 04 moved up to third on 13 points following their 1-0 win over rivals Borussia Dortmund, while Bayern drop to sixth on 11 points.
Bayern began the match with chief strikers Miroslav Klose and Mario Gomez on the bench but they still might have taken an early lead when Franck Ribery fed Arjen Robben on the left to put a low drive just wide.
The entry of Hamburg striker Marcus Berg for defender Guy Demel in the second half immediately lifted the pace with the hosts threatening several times before former Hamburg striker Ivica Olic's point-blank shot was saved.
Ze Roberto, the 35-year-old Brazilian who left Munich in the close season after Bayern proved unwilling to give him a new two-year deal, finally managed to split open the visiting defence when he set up Petric in the box for an easy tap-in.
Bayern substitute Klose did put the ball in the net six minutes from time but his effort was ruled out for an offside.
"Before the match we were top of the table and everyone spoke about a crisis," said Hamburg coach Bruno Labbadia in reference to their mid-week German Cup exit to third division Osnabrueck.
"Well today this was a super response and even more so against a team as strong as Bayern," he told reporters.
LEVERKUSEN WIN
A late goal from Simon Rolfes earned Bayer Leverkusen their victory over Cologne.
Rolfes picked up a pass from Tranquillo Barnetta, raced into the box and beat two defenders before firing in the winner off the post with eight minutes to play.
Cologne, toothless throughout, finished with 10 men after Maniche was sent off for kicking Arturo Vidal late in the game.
Schalke won the big Ruhr valley derby in Dortmund thanks to a first-half strike by Jefferson Farfan, a result that took them up to third place on 13 points.
Farfan struck after half an hour and against the run of play when Levan Kenia launched a quick counter-attack and found Halil Altintop on the left. He cut back and set up the Peruvian striker to slot home his third goal of the season.
Champions VfL Wolfsburg defeated Hanover 96 4-2 to move up to fifth, on 12 points. Werder Bremen, who also have 12 in fourth place, beat promoted Mainz 3-0 with Claudio Pizarro scoring two.
