The 29-year-old is facing seven months on the sidelines after damaging the anterior cruciate ligament in his right knee moments after volleying home the only goal of Sunday's (AEST) 1-0 Bundesliga win over Augsburg.
Muller wheeled away in celebration, performing helicopter whirls before leaping into the air.
He landed awkwardly, collided with the corner flag and collapsed to the turf in pain.
"I slipped with my right leg, unfortunately, after my usual helicopter celebration," he said.
"I injured myself at the knee, it was so stupid."
A trip to Cologne is next on the agenda in the Bundesliga for Hamburg on Saturday, as Muller begins his lengthy rehabilitation.