The Manchester United manager said that he felt the need to grant the 31-year-old's request to move back to his boyhood club after a 13-year tenure at Old Trafford.
Rooney was officially announced by the Merseyside club on Sunday, signing a two year deal to return to Goodison Park.
"It is no secret that I have long been an admirer of Wayne; he has been a model professional throughout his time at the club and will remain in the history books for many years to come," Mourinho said in a statement posted on United's official website.
"It is never easy to see a great player playing less football than he would like and I could not stand in his way when he asked to go back to Everton.
"His experience, focus and determination will be missed and I wish him well for the future."
Ed Woodward, United's executive vice-chairman, added to the plaudits.
"Wayne has been a fantastic servant to United since the moment he signed for us as a prodigiously talented, explosive teenager some 13 seasons ago," Woodward said.
"On behalf of the whole club and our hundreds of millions of fans around the world, we wish Wayne all the very best for the next phase of his incredible career."