The midfielder was sent off in the first half of the champions' 3-0 defeat at West Brom after kicking the ball against Chris Brunt's head from 20 yards away.
Referee Mike Jones was taking control of a spat between Diego Costa and Gareth McAuley when Fabregas kicked the ball back towards the group.
The former Barcelona man was dismissed as a brace from Saido Berahino and Brunt's strike sealed victory for Albion.
Fabregas is staring at a ban and Mourinho was left wondering why, following Chelsea's third defeat of the season.
He said: "Where is the danger of the situation, where is the aggression in the situation to get the red card in a friendly game?
"I really don't understand
I think (Darren) Fletcher was aggressive, he pushed him (Fabregas) in the chest because he is experienced and knows where he can push for a yellow card
He is much more aggressive than what Fabregas did.
"For me a top referee, a stable, big personality and in control of the game, goes there, two or three words and it's done
It's a bizarre red card.
"A three game ban for this? Harsh? Of course it's harsh
Why does he have to explain? He doesn't need to explain."
Despite defeat, Chelsea will still lift the Barclays Premier League crown on Sunday after their home game with Sunderland.
And Mourinho refused to blame his players and took a sly dig at their title rivals for allowing them to switch off at the end of the season.
He said: "The ideal scenario is to be champions and don't play again, go home have holidays and don't play again.
"When you have three more matches to play it can happen what happened to Bayern Munich, lose three in three
It can happen to us, one point in two matches.
"I don't blame the players, to blame the players I have to blame myself because I am not different than them.
"Let's blame the players a little bit, let's blame myself, let's blame the top contenders for the title because they were not good enough to fight with us until the end.
"If today we need this game to be champions, I'm not saying we'll win but I'm saying we would compete at a higher level to win."
The Baggies clinched a deserved victory though and their most impressive under Tony Pulis.
The boss took over in January when they were a point above the bottom three and Albion are now 10 points clear ahead of Sunday's finale at Arsenal.
He said: "I'm really pleased, it was a great result, a great performance
On the night we are very, very pleased
It's a great finish but I don't think anything should be taken away from the team we've played.
"They have been by far the best team in England, they won it by a country mile and have been that better than everyone else.
"Although we won on the night, all the praise should go to Jose, his coaching staff and the players."
Source : PA
Source: PA