A double-blow inflicted by Bruno Fernandes inside seven first-half minutes ended Everton’s Goodison Park unbeaten record.
Carlo Ancelotti’s side had claimed seven points from nine at home before this and won two cup games on their own ground, too.
And they looked to be responding to successive away losses exactly as manager Ancelotti would have ordered when Bernard, starting in the Premier League for the first time since 16 July, swished a low drive beyond David De Gea.
It wasn’t only their goal creating the impression Everton were in the ascendancy.
Ancelotti’s team were comfortable in a disciplined structure and looked capable of hurting Ole Gunnar Solskjaer’s side, especially when Bernard and Lucas Digne joined forces on the left.
United are packed with quality players, though. Marcus Rashford and Fernandes are two of them and, with Fred influential in midfield, that pair began turning the tide.
Fernandes scored with a header on 25 minutes, adding a second less authentically seven minutes later with a cross which drifted beyond its intended target in Rashford but reached the back of the net nonetheless.
Ancelotti tweaked and finessed during the second half, altering his personnel and formation.
And we had a reminder of the margins which decide a lot of Premier League matches deep into stoppage time.
Alex Iwobi did wonderfully well to volley a cross into the centre but Abdoulaye Doucoure, straining to make contact, missed his kick.
In the blink of an eye Manchester United were at the other end, Edinson Cavani sweeping in with the final kick.
Everton were fifth at the final whistle. They have two weeks to lick their wounds before going to Fulham.
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ANCELOTTI PINPOINTS KEY IMPROVEMENT EVERTON MUST MAKE
Everton went route one to go in front.
But once Bernard, showing tremendous anticipation, received Victor Lindelof’s untidy header – the defender under pressure from Dominic Calvert-Lewin after Jordan Pickford’s long punt – the Brazilian’s skill and imagination were the only story in town.
Cushioning the ball with the outside of his right boot, Bernard escaped Aaron Wan-Bissaka to deposit his strike low past De Gea’s right hand.
It was Bernard’s first Premier League goal since he scored in a win over Crystal Palace in February.
This happened in the 19th minute but even so early it was fair comment to declare Everton deserved their lead.
Obviously sitting off when United had the ball to deny the visitors the space they crave for counter attacks, Everton sprang into life in possession.
James Rodriguez waited only six minutes to spear his favourite pass for left-back Digne, who ushered in Bernard.
The forward’s cross was directed at Calvert-Lewin, darting in front of Harry Maguire but heading too high.
James, flush with confidence and his rhythm apparently undisturbed after missing Everton’s visit to Newcastle last week, twice brought his individual tricks to the party.
There was a header directed down the line with James’s eyes fixed firmly infield to deceive his opponents, while another flick sent Seamus Coleman into United’s penalty box unchallenged.
Digne fizzed over a cross which Maguire cleared shortly after and it felt like Everton were exerting a firm grip.
That suspicion grew with Bernard’s goal but by the time the scorer was providing a return pass for Digne to run forward and crack the outside of the near post with a drive, United had levelled.
Fair warning of the away team’s threat had arrived when Anthony Martial swiped a shot wide after controlling Fred’s lobbed ball into the box and drilling across goal.
Allan had flung himself in front of a Fernandes drive, too, the rebound looping up for Rashford whose odd connection sent the ball on a looping trajectory, landing on the top of the net.
Rashford was off-target after being picked out wide on the left by Scott McTominay and stealthily progressing closer to goal to aim at the far post.
England forward Rashford was involved at the outset of his team’s equaliser, Juan Mata gathering the pass to feed Luke Shaw.
His cross, lifted into the centre, was met smack on the forehead by the motoring Fernandes for a finish which travelled inside Pickford’s left post.
Indeed, not a lot had been asked of Pickford until now, the goalkeeper’s chief concern the low sun obscuring his vision.
There was nothing he could do about Fernandes’ header – nor the Portuguese’s second goal seven minutes later.
Between times Pickford watched a Fernandes free-kick all the way into his gloves.
But when the midfielder found the net 60 seconds later, Pickford was helpless again.
Fernandes wasn’t trying to score, rather locate Rashford with a cross from the left.
Rashford leapt but didn’t connect, the ball continuing unmolested on its path to nestling inside the far corner.
Everton turned the possession tables immediately after the restart, United taking their turn to bunch behind the ball.
Coleman took it upon himself to burst through the massed red shirts – after a fabulous first touch when James sent a pass inside – but found one defender too many blocking his route to goal in the shape of Lindelof.
Iwobi’s introduction for Gylfi Sigurdsson meant a midfield role for James and an opportunity for the Colombian to employ his passing range.
He landed balls from deep on the toes of Iwobi and Digne in quick succession, without Everton being able to create the opening they urgently required.
So urgently, in fact, that United’s counter was in play for the first time and Pickford had to spread himself to deny Rashford when the United forward ran onto Fred’s ball through the middle.
Mason Holgate swung his boot to clear a Mata effort – and the contest was becoming more open than at any point.
Maguire did very well to head away from danger when Calvert-Lewin appeared set to meet a terrific right-wing cross from Iwobi.
James, perhaps running out of gas following his enforced break, made way for Cenk Tosun to make a second appearance from the bench in successive weeks.
This was Ancelotti twisting, going with two up front.
Which meant a collective effort to get back in shape when United threatened.
Seven defensive bodies hurtled back behind the ball as the away side tried to break from an Everton corner, Iwobi eventually relieving Rashford of possession.
A Digne free-kick – after another driving Coleman run was illegally ended – landed on the head of Maguire.
Everton’s full-backs were having a big say.
Coleman rolled Fred to tee up Doucoure in stoppage time but the midfielder was too high with his shot from 18 yards.
Doucoure had one final half-chance but, really, would have needed a slice of luck for Iwobi’s improvised volleyed delivery to fall right for him.
United broke and, at the last, sourced joy on the counter, Uruguayan Cavani steering into the Park End net.