كتب : Hatem Maher
The prolific Dutch marksman has failed to recover from a thigh injury in time for the game, Hamburg said on their official website.
"I really wanted to play against Bayern Munich, but I won't make it in time," Van Nistelrooy, who also missed Hamburg's Europa League clash against PSV Eindhoven on Thursday, said.
"I'm not yet fully fit and it wouldn't make any sense to include me in the match squad."
Van Nistelrooy joined Hamburg in the January transfer window after a succession of injuries limited his first-team opportunities at Spanish giants Real Madrid, where he enjoyed a fruitful four-year spell.
He scored two goals in his second appearance with the six-time German champions to help them defeat Stuttgart 3-1 earlier this month.
Hamburg lie fourth in the Bundesliga table with 40 points, nine behind joint leaders Bayern and Bayer Leverkusen.