The Dutch winger, already yellow-carded for a foul ran to Chelsea supporters to celebrate his goal and Chelsea's winner in a 2-1 victory over Sunderland.
But ref Chris Foy decided to give the mercurial wide-man a second yellow and red and dismissed him from the field.
Mourinho said: "Under the rules, the referee had no option. I don't like the rule because part of the show is the players' relationship with the crowd.
"Arjen has to learn when he already has a yellow card, he has to control himself," the manager added.
"It's an experience for him, next time he has a yellow card and scores he has to make sure he stays on the pitch.
"He will not do it again. He will remember for his career because he has had a yellow card that he cannot celebrate with the fans when he scores a goal."
He added: "I think it would be easy for a referee to give one more minute extra-time instead of the second yellow card.
"The player celebrates with the fans, it takes a little bit more time - instead of three minutes extra time, he gives four or five and it's done.
"But I think referee Chris Foy did well because he did what the rule says he had to do.
"It's a chance for Damien Duff and Shaun Wright-Phillips to play the next game because Arjen will be suspended."