Chelsea have had two bids for Rooney rejected by United, despite Moyes having admitted during the summer that Rooney is only needed as back-up for Robin van Persie.
Rooney has been openly glum in his appearances for United recently - with a memorable photo from last week of Rooney avoiding a celebration with team mates saying it all.
And Mourinho pulled no punches when asked if Moyes was the man to blame for Rooney's unhappiness.
"Of course," he replied. "We are trying to get a player that a manager told 'You will be a second option' for him.
"We are not going for Van Persie. They [United] don't have to be against me. If I say Ramires is a second option for me and he plays when Lampard is tired or injured, if someone comes here to get Ramires, nobody is upset.
"In every big team, I am not criticising, you have first options and second options, and those second options must be very good players.
"Of course big teams must have second choices. Big players too. The point is if the players are happy to accept that situation."
Mourinho then clearly reiterated that Rooney would not have to accept being a number two at Stamford Bridge, and pointed out that it is only the strength of United's strike force that has left Rooney in the cold.
"It means they have a fantastic squad," Mourinho added. "Fantastic. I was playing against them last year. He was on the bench and [Alex Ferguson] was playing Van Persie, Welbeck, Kagawa. The squad is amazing. So it is natural that some players have to be second-choice."