Earlier in April, Bayern scored twice in the final moments of the last-eight second leg at their Allianz Arena home to seal their spot in the semi-finals.
A group of fans from the Bayern ultras section climbed over barriers while celebrating, trampling pitch-side photographers.
One photographer reported a concussion while another suffered a head laceration, with others also needing medical treatment.
The governing body fined Bayern a total of 89,625 euros, breaking the penalty down into 40,000 for spectator disturbances, 30,000 for a fan banner critical of UEFA, 14,000 for blocking aisles and 5,625 for throwing objects.
Despite the threat of a fan lockout for the second semi-final leg against Paris Saint-Germain, Bayern were confident of a full house.
"We expect to be able to celebrate a football festival with a full stadium against Paris," sporting director Christoph Freund said prior to UEFA's decision.