Mourinho was quick to blame the official in charge for his side's defeat, Jonas Eriksson, whom he felt was wrong to dismiss Chelsea midfielder Ramires for a second yellow card folllowing a challenge on Mario Gotze.
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"I thought Mourinho's statement was outrageous," Rummenigge told Bild.
"After a horrible tackle like this, Mario can consider himself lucky. The injury could have been much worse."
Hoeness, meanwhile, was equally surprised with Mourinho's criticism of the referee.
"That was the clearest red card ever," the Bayern president said.
"If a coach like Mourinho then starts talking about a wrong decision, I ask myself if he maybe attended the wrong game."
The Bundesliga representatives won 5-4 on penalties (2-2 AET) on Friday.
Meanwhile, Gotze will be out of action for at least three weeks because of the injury he sustained following Ramires' tackle.