The England international, who has had to cope with revelations about his private life all week, was not on the team coach when it arrived at the ground an hour and 15 minutes before kick-off and his name did not appear on the team sheet.
Rooney was reportedly at the team’s hotel in Manchester last night and there was a suggestion he may have travelled independently but Alex Ferguson’s selection dispelled that theory.
As a result the England striker has been replaced in the team by Gary Neville as the only change from the 3-0 victory over West Ham prior to the international break – meaning there was no comeback for centre-back Rio Ferdinand who did not even make the bench.
Everton manager David Moyes has made two changes from the side which lost at Aston Villa, with Leon Osman replacing Jack Rodwell, who has been ruled out for at least two months with a knee injury, and John Heitinga coming in for Jermaine Beckford.
That means the hosts began the match with no recognised striker, with Louis Saha sidelined by knee problems again.
Everton: Howard, Hibbert, Jagielka, Distin, Baines, Osman, Heitinga, Arteta, Pienaar, Fellaini, Cahill.
Subs: Mucha, Bilyaletdinov, Beckford, Neville, Gueye, Yakubu, Coleman.
Man Utd: Van der Sar, Neville, Vidic, Jonathan Evans, Evra, Scholes, O’Shea, Fletcher, Nani, Berbatov, Giggs.
Subs: Kuszczak, Owen, Smalling, Park, Rafael Da Silva, Macheda, Gibson.
Referee: Martin Atkinson.