The Portuguese coach had just watched his side exit the competition 4-3 on aggregate after a frantic 2-0 win at the Bernabeu.
He apportioned blame to Webb for not awarding a free kick and sending off Mats Hummels for a handball on the edge of the area.
"I am very sad and disappointed with one of my favourite referees, Howard Webb," Mourinho told ITV Sport.
"It's a red card for Mats Hummels, he saw it. In that moment he was not a referee, he was a human being.
"He thought 'if I give a red card to Mats Hummels, he will miss the final'."
The 50-year-old also suggested that he would be leaving Real to join Chelsea this summer.