Bastian Schweinsteiger needed 12 minutes to open the scoring and put the hosts in front.
His shot from inside the area bounced off the turf and went into the net after Hamburg defense failed to clear a Ze Roberto cross.
Lukas Podolski doubled Bayern's advantage four minutes later when he converted a penalty after defender Joris Mathijsen was adjudged to have fouled Schweinsteiger.
Peruvian striker Paolo Guerrero pulled one back for Hamburg in the 25th minute after he rose unmarked to head home a right-wing cross past Michael Rensing.
Rensing has been Bayern's first-choice goalkeeper since the retirement of Oliver Kahn following last season's end.
Lively midfielder Piotr Trochowski leveled the score in the 56th minute from the penalty spot.
Egyptian forward Zidan did not take part in the game as Hamburg coach Martin Jol preferred to put him on the bench.