Khedira, making his first appearance of the season after injury, was shown a second yellow card shortly before halftime after getting caught up in a melee and shoving the home side's captain Sergio Ballesteros to the ground.
Portuguese Mourinho accused Levante of baiting his players but said Khedira had shown a lack of intelligence by reacting as Real suffered their first setback of the campaign following wins in their first two games.
"The blame in my opinion lies with one of my players who was lured into a trap," Mourinho told a news conference.
"In part he is responsible for the defeat, I have no problem in saying it, but the referee also shares the blame, as do I and the players," the former Inter Milan and Chelsea manager added.
Mourinho, who joked before the game that Real's priority this season was to avoid relegation, said he and the players had studied videos of similar situations that had led to red cards as part of their preparation for the match in Valencia.
"I thought that this would not happen and that nobody would get a red," he said.
"You prepare and then later the response is not the one you want. I think the players have to prepare themselves.
"They have to have enough intelligence to avoid situations like that and have a sense of whether the referee will allow it or not.
"That's why I have to congratulate Levante for being clever, because they know how to provoke, simulate, not give back the ball, waste time, and that is also part of football."
