After a shock 3-2 defeat to Crystal Palace midweek Everton needed to take all three points from the match in order to keep pressure on Arsenal for that Champions League place.
Despite sitting in seventh, United had a good away record and have won three of their last four Premier League games.
United were missing experienced players such as Nemanja Vidic and Patrice Evra, which perhaps showed as despite having the greater possession United conceded two goals without creating many opportunities of their own.
Wayne Rooney had United’s best chance late on but Tim Howard made the save to keep Everton in fifth, still one point behind Arsenal.
The Red Devils look unlikely to qualify for even the Europa League and must now be looking forward to wrapping up this disastrous season.