Leighton Baines stepped up and made no mistake with a clinical spot-kick that he drilled straight down the middle.
The visitors struggled to carve out clear-cut chances and were undone on the counter two minutes before the break when Kevin Mirallas beat the offside trap to coolly drill home.
Everton eased through the second half and could easily have added to their tally with Steven Naismith twice going close to extending the advantage.
The defeat mathematically ends United's hopes of reaching next season's Champions League, while Everton remain just a point behind fourth-placed Arsenal with three games to play.
PRE-MATCH: JAGIELKA still out, Nani returns: Steven Naismith and James McCarthy are the two changes made by Everton following the home loss to Crystal Palace. John Stones continues to deputise at centre back in place of injured captain Phil Jagielka. Wayne Rooney skippers United in the absence of Nemanja Vidic while Nani makes a rare start following a season plagued by injury. Ex-Blue Marouane Fellaini is left on the bench.
9' - EVERTON CHANCE! Coleman's cross is nodded into the path of Ross Barkley by Smalling but the England midfielder fluffs his volley and skies it into the stand.
22' - EVERTON CHANCE! Sylvain Distin hoists a long free kick towards Lukaku who nods it down for Naismith, but the Scot crashes over on the volley from just inside the box.
28' - GOAL! Everton 1-0 Man United. Phil Jones handles Lukaku's shot and the referee inevitably points to the spot. Baines steps up and lashes the spot kick down the middle as David De Gea dives to his right.
43' - GOAL! Everton 2-0 Man United. Coleman plays Mirallas clear as United fail to spring the offside trap and the Belgium winger makes no mistake with a thumping finish into the far corner.
77' - It should be three. Mirallas surges down the right and drills a low cross to the far post where Naismith somehow contrives to volley over the top.
80' GREAT SAVE! Coleman leads an Everton counter and tees up Naismith who sees his low shot tipped past the post by De Gea.
87' - WHAT A STOP! Rooney breaks clean through on goal but sees his shot brilliantly kept out by the flailing hand of Howard. Wonderful stop.
TALKING POINT: Can Everton still get fourth? The Toffees remain a point behind Arsenal with three games to play. The Blues appear to have the more difficult run-in but if the Gunners slip up, you wouldn't bet against Roberto Martinez and co on this evidence.
David Moyes once again named a different starting XI for Man Utd (51 games, 51 unique teams).
Everton scored in both league games against Manchester United for the first time since 2003-04.
Leighton Baines has scored all 13 of his Premier League penalties, the only player to take over 10 spot kicks and have a 100% record.
Everton have completed a league double over Man Utd for the first time since the 1969-70 season.
The Blues have now won 20 league matches so far this season, their highest number of victories in an entire Premier League campaign ever.
Man United have only won one of their 12 games this season against the league's current top six.
(Stats courtesy of Opta Joe)
MAN OF THE MATCH
Seamus Coleman (Everton): A stunning display from arguably the best attacking full-back in the league. A constant menace throughout and solid in defence when called upon.
PLAYER RATINGS -
EVERTON: Howard 8, Baines 8, Distin 7, Stones 7, Coleman 8, McCarthy 7, Barry 7, Mirallas 8, Barkley 7, Naismith 7, Lukaku 7. Subs: Alcaraz 7, Osman 6, McGeady n/a.
MANCHESTER UNITED: De Gea 7, Jones 4, Evans 6, Smalling 5, Buttner 5, Carrick 6, Fletcher 6, Nani 6, Mata 6, Kagawa 6, Rooney 6. Subs: Valencia 6, Hernandez 5, Welbeck 5.
MATCH IN A TWEET
- Sports & Recreation
- Manchester United
- Steven Naismith
- Leighton Baines
- Phil Jones
- Kevin Mirallas
- Romelu Lukaku