A sublime David Beckham free-kick and a dubious penalty from Ruud van Nistelrooy shattered Everton's hopes of European football as United finished the season with a flourish.
Everton looked sharp in the first half and the Blues were ahead as early as the seventh minute.
Thomas Gravesen swung in a corner from the right and Kevin Campbell rose above the Manchester United defence to nod home a simple header.
But Manchester United were oozing confidence, played patient football and carved numerous chances.
On ten minutes, Wes Brown crossed to van Nistelrooy who coasted round the back of the Blues defence, but fired his point-blank header into the arms of Richard Wright and the Dutchman missed a glorious chance to equalise on 23 minutes as he scooped his shot over Wright after being played in by Beckham.
Wayne Rooney bamboozled United's defence, turning Rio Ferdinand inside out, before firing a shot from distance which was well saved by Roy Carroll.
David Unsworth up-ended Ole Gunnar Solskjaer on the edge of the box on 42 minutes and Beckham eventually found United's equaliser.
From what looked like an impossible angle the England captain dipped a superb free-kick over the wall into the left-hand corner.
After the break United continued to pile on the pressure as Wright had to be on fine form to keep out a second but it was everyone's wonderkid Rooney who missed two sitters to the astonishment of the Blues fans.
Gary Naysmith whipped a ball across the face of goal on 51 minutes, but an unmarked Rooney sidefooted wide when it was easier to score, even the scoreboard flashed goal and had to be corrected later.
United eventually sealed three points on 74 minutes when van Nistelrooy tumbled under the challenge of Alan Stubbs for a contestable penalty.
Van Nistelrooy slotted home with style and United played kick-ball until the final whistle.
After the match United eventually lifted the Premiership trophy to the delight of the visiting fans as Everton ponder how European football has eluded them.