The former England skipper returned to his former ground with Everton in his first appearance against United, with whom he spent a successful 13 years, since re-joining his boyhood club in July.
Rooney, who was substituted with eight minutes remaining when the deficit was just one, was afforded a huge ovation by the home supporters.
Mourinho insisted that he was not surprised to see the forward receiving a warm welcome at the Old Trafford by the club's fans.
"It is the nature of English fans and big clubs when a player is big in the club and has an important part of the club's history," goal.com quoted the United boss as saying.
"He is at home and one day I believe he will be back home," he added.
Rooney scored 253 goals for United in his 13 years at the club. (ANI)