Anthony Martial's 54th minute strike proved to be the difference in a keenly contested affair and continued a largely frustrating season for Roberto Martinez's side.
Everton's miserable season and Old Trafford record continues
In the corresponding fixture in December 2013 Bryan Oviedo was the hero as Everton beat Manchester United at Old Trafford for the first time in 21 years. That victory came in David Moyes' only season at Old Trafford and highlighted Manchester United's decline post-Sir Alex Ferguson and the optimisim at Everton under Roberto Martinez.
The 2013/14 season saw Everton finish fifth in the table and record their highest Premier League points tally. However, fast forward two years and the optimism has been replaced with a mood of frustration as supporters patience and tolerance with Martinez dwindles even further.
Sunday's defeat to Manchester United was their tenth Premier League loss of the season, albeit only their second defeat away from home, leaving the Toffees 12th in the table, closer to the relegation zone than the top-four. And with Martinez's side languishing in mid-table many people would expect the Blues to play with more freedom as they play for their futures rather than position.
This should have been a performance with quick counter-attacking football, chances aplenty and goals, especially considering Martinez's bold team selection of opting for two wingers in Gerard Deulofeu and Aaron Lennon. However, the Blues were missing the key ingredient of a cutting edge. Too many promising forward movements collapsed on the back of imperfect final balls.
Heading into the weekend Everton may have been the most clinical side in the top-flight having scored with 18 per cent of their goal attempts this campaign. However, in a match where chances were at a premium for both sides, the Blues managed just one shot on target over the entire 90 minutes.
With Romelu Lukaku isolated for most of the match, Everton's best attacking threat proved to be the unlikely Phil Jagielka. The Blues defender and captain saw his header ricochet off the crossbar; moments after Martial had put United ahead, before David de Gea produced a great save to deny Jagielka again with Everton's only shot on target.
There will be no second chances at Wembley
Everton could meet Manchester United again on Saturday 23 April at Wembley in the FA Cup semi-final where the Blues will be hoping for revenge, but first Louis van Gaal's side must beat West Ham United in their replay on Wednesday evening.
The continuation of the Toffees' miserable season makes the FA Cup semi-final undoubtedly the biggest match of Everton's season and arguably the biggest game of Roberto Martinez's Everton tenure. The FA Cup could be a saving grace for Martinez and his players can still save this season from the jaws of failure, but this can only be achieved if Everton win the FA Cup.
Should Everton play Manchester United in the semi-final then they are going to have to quickly learn lessons from their Old Trafford defeat, because the Toffees did not do enough to win. Everton supporters will want to see more cutting edge and adventure from their side in the semi-final, especially as there will be no second chances at Wembley as they look to rescue their season from being a complete disaster.
John Stones shows his credentials
It is always hard to spot positives in a defeat, especially after three successive defeats, but it was not all doom and gloom for the Toffees at Old Trafford. There was much to admire about their first-half performance; the Blues pressed well, defended with assurance and showed intent.
However, they could have easily been behind at half-time if John Stones had not shown his credentials. The 21-year-old, making only his second club start since January, has been under "incredible scrutiny", according to Roberto Martinez, over recent weeks. But the centre-back showed plenty of confidence on the ball and made a superbly timed challenge to deny Martial in the first-half to keep the score goalless at half-time.
The Everton boss will have been pleased with what he saw from Stones after bringing him into the starting XI in place of Ramiro Funes Mori and he will be hoping to see more of the same from the young defender.