The Toffees responded to Arsenal winning earlier on Sunday with first-half goals from Leighton Baines and Kevin Mirallas in David Moyes's first game back at Goodison Park since leaving to become United manager.
Defeat officially confirmed that United won't be participating in next season's Champions League and here, Sports Mole takes a closer look at the action on Merseyside.
On target: 5
On target: 2
Was the result fair?
Absolutely. Even though United restricted Everton to their lowest possession count of the season, it never really felt like the Red Devils were on top. Everton had so much more electricity going forward and ran out deserved winners.
Often this season the Toffees have been the team patiently probing but today they were on the receiving end of that style of football. Roberto Martinez's players adapted really well and were so dangerous on the counter-attack. Right-back Seamus Coleman has been a standout player this season and today he was everywhere, breaking up United's attacks and then starting breaks upfield on several occasions. Another player to shine was James McCarthy, who kept it tight in front of the backline and restricted the creativity of the likes of Juan Mata and Shinji Kagawa.
Man Utd's performance
After scoring eight goals in their previous two league games, United looked completely out of ideas offensively today. Former Toffee Wayne Rooney was employed as the main striker and very rarely troubled the Everton defence. Considering how much possession they had, United created hardly any clear-cut chances and that simply isn't good enough when you compare how many shots Everton had. Phil Jones will look back and wonder what he was thinking when he flailed his arms in the air and blocked Romelu Lukaku's shot with his arm to concede the penalty that Baines tucked away. It was another defensive error that led to the third goal as Alexander Buttner lazily played Mirallas onside.
Sports Mole's man of the match
Seamus Coleman: Without a doubt the star of the day, the Irish full-back never ran out of steam and constantly gave United a headache down the right-hand side. His pass into Mirallas for the second goal was perfectly weighted.
You have to look at Jones for the way he carelessly raised his arms to concede the penalty. Rooney was also culpable for a bad miss late on which he should have easily tucked past Tim Howard.
Everton fans don't like Mark Clattenburg but will have no complaints about his performance today. He correctly pointed to the spot when Jones handballed and then played advantage in the lead-up to the second.
Everton: The Toffees have a tough run-in and next travel to Southampton on Saturday lunchtime.
Man Utd: United, meanwhile, host ailing Norwich City on Saturday evening.