United welcomed back Nemanja Vidic, Ryan Giggs and Phil Jones to their starting line-up, while Phil Neville came in for Sylvain Distin for Everton after the Frenchman was injured in the warm-up.
United should have taken the lead early on when Rooney released Robin van Persie, but the Dutchman somehow hit the post after rounding keeper Tim Howard.
However, Van Persie made amends three minutes later when he shrugged off his marker and fed Ryan Giggs, whose low shot found the net via the inside of a post.
The visitors responded well to going behind and carved out a couple of chances, but having failed to make the most of them paid the price right on the stroke of half-time.
Rafael sent Van Persie racing away from a square Everton backline and the striker this time rounded Howard and found the net, despite the best efforts of the covering Johnny Heitinga.
The early part of the second half saw both sides struggling to create further chances, but just past the hour mark United came close to adding a third goal.
A corner from the right was headed on by Jonny Evans, who saw his initial effort and a follow-up blocked by Howard, before sub Nikica Jelavic blocked a third strike from Evans.
Within seconds Howard finger-tipped away a Tom Cleverley volley, before the game drifted to an inevitable conclusion in the closing 20 minutes.