Rooney did not even travel to Goodison Park as manager Sir Alex Ferguson, on the occasion of his 700th Premier League match, claimed he wanted to protect the 24-year-old from abuse from the fans with whom he used to be a favourite.
The disruption appeared to affect his team-mates early on as they fell behind to a Steven Pienaar goal but Darren Fletcher, Nemanja Vidic and Dimitar Berbatov put United well ahead before the Toffees' stunning late comeback through Tim Cahill and Mikel Arteta.
Ferguson has overseen plenty of player controversies during his lengthy tenure at Old Trafford, dealing with the likes of David Beckham's celebrity lifestyle and Roy Keane's unique brand of criticism.
However, leaving out a player to protect him from opposition fans is unprecedented and surely unlikely to be repeated.
Whether it affected the overall result is open to debate but when the England international next appears, likely to be in Tuesday's Champions League clash against Rangers he will get nothing less than a rousing Old Trafford reception.
Rooney's absence seemed to affect United more than they expected as, for the first 15 minutes, they found themselves under constant pressure.
Arteta's sixth-minute free-kick was tipped over by Edwin van der Sar, although referee Martin Atkinson did not spot the goalkeeper's touch.
The Spaniard had another shot deflected behind by Jonny Evans, Pienaar saw his shot from the Spaniard's corner blocked and Leon Osman blazed over all in the same passage of play.
Ferguson was less than happy and was soon prowling his technical area barking orders at the players.John O'Shea's response was a blistering drive from the left angle of the penalty area which grazed the outside of Tim Howard's left-hand post.
Everton's pressure, albeit slightly less intense, continued while Nani was off the field having a cut lip tended with Cahill, Marouane Fellaini and Leighton Baines all failed to trouble the goalkeeper with half-chances.
There was always the danger their failure to capitalise on possession would leave the way open for United to nick a goal and they almost did in the 34th minute.
Tony Hibbert's foul on Ryan Giggs, despite winning the ball, saw Nani roll the free-kick to Paul Scholes and his powerful drive took a big deflection off Cahill but Howard, diving in the opposite direction, somehow diverted the ball over with his foot.
Four minutes later the American goalkeeper stuck up a hand to palm away Giggs' close-range shot after United counter-attacked.
But the visitors were caught cold themselves when Patrice Evra missed an ambitious overhead-kick clearance to put Arteta charging through on goal and although he shot straight at Van der Sar, Leon Osman turned the rebound to Pienaar at the far post who rolled home.
Two minutes before half-time, however, Nani's cross was diverted home by Fletcher and Berbatov's volley almost put them ahead in added time.
It was apparent at the start of the second half Everton were in for a tougher test and it took just three minutes for that to become a reality.
Nani's corner from Berbatov's deflected shot was only half-cleared and when Scholes returned the ball to the Portugal international wide on the right he swung over a cross for an unmarked Vidic to head in from five yards.It at least provoked a reaction from Everton and Pienaar's curling 20-yard shot was held by Van der Sar at the second attempt.
But United were where they like to be, in control and able to counter-attack, and one rapid foray forward saw Howard deny Nani low to his right.
He got nowhere near the next one in the 66th minute, which owed everything to the brilliance of Scholes and Berbatov.
The former England international's raking pass picked out the Bulgarian wide on the right and his first touch brilliantly took him clear of Sylvain Distin.
With acres of space to run into the languid striker took five or six paces before lashing an early shot into the bottom corner, taking Howard by surprise.
Baines curled a free-kick into the side-netting and as Osman hit a woefully-weak shot at Van der Sar as the hosts tried to find a way back but, as has been the case in their previous matches, they lacked a cutting edge.
However, in a dramatic finish Cahill headed home in injury-time before Arteta's deflected strike snatched an unlikely point.
Source: Manchester Evening News