The Swede scored a 94th minute penalty after Ashley Williams had handled Luke Shaw’s goal bound strike but United are now four points off the top-four having played a game more.
“If you are losing 1-0, you need to make changes and the coach sees that. We were much better in the second half,” Ibrahimovic said afterwards.
It took their Premier League unbeaten run to 20 games but they have now dropped 20 points at Old Trafford and Jose Mourinho may now have no option but to switch all his focus to the Europa League in a bid to secure Champions League football for next season.
It was heartbreak for Everton after they bounced back well from their Merseyside derby disappointment on Saturday. Phil Jagielka’s scrappy strike had given them the lead and they defended expertly until one slip deep in injury time.
Mourinho was furious with his forwards after United’s stalemate West Brom on Saturday but won’t have been any happier with their reaction against Everton.
Ibrahimovic and Ander Herrera were brought straight back into the side after serving suspensions with Henrikh Mkhitaryan and Anthony Martial dropping to the bench while Wayne Rooney couldn’t even make the 18-man squad to face his former club after an ineffectual 10-minute cameo against the Baggies.
Rooney’s absence was startling given the lack of attacking options on the bench particularly as Shaw, whose days at Old Trafford look numbered, was named as one of the substitutes.
The decision to leave out Mkhitaryan was also a shock given his form in the recent months.
The summer signing was axed for three months after a substandard performance in the Manchester derby in September and Mourinho clearly believes his levels have dropped again.
“The thinking is because I am not happy with Mkhi’s performance in the last match,” Mourinho said before the game.
Mkhitaryan and Shaw were given their chance with 25 minutes to go, the latter making a decisive impact, when were United already trailing and the players who kept their places looking woefully short of confidence rather than inspired by their public rollicking from their manager.
Jesse Lingard buzzed around without making any impact; Marcus Rashford looks like a teenager who hasn’t scored in the Premier League since September and failed to hit the target even when he was two yards’ offside, while Marouane Fellaini was pushed further forward and was an ineffectual passenger against his former club.
Even recalled top-scorer Ibrahimovic, who has sat out the last three domestic games after a stray elbow in the draw with Bournemouth, looked sluggish when he was presented with the first opportunity; dawdling as he closed in on goal and Ashley Williams was able to get back to challenge.
They fell behind in the 22nd minute with a goal that keeper David de Gea won’t want to see again.
The Spaniard, who was sporting a new, closely cropped haircut, initially turned away a low shot from Kevin Mirallas at his near post. But from the resulting corner, Williams’ header looped to Jagielka in the six-yard box and his weak hooked effort bounced through De Gea’s legs.
Mourinho looked furious with his side as he stood silently on the edge of his technical area with his hands in his pockets — unusually motionless even when Neil Swarbrick gave a contentious decision against his side and rolling his eyes towards the Stretford End when a free-kick from Daley Blind failed to make it beyond a one-man wall.
They at least got an effort on target in the 30th minute from the next free-kick but Joel Robles, fresh form his Merseyside derby nightmare, clawed away Blind’s 20-yard strike and Herrera then clipped the crossbar with the follow-up from a tight angle.
Mourinho’s response was to throw on Paul Pogba — back after a minor hamstring injury — at half-time and the world record signing went close to pulling his side level in the 54th minute.
But his header from an Ashley Young free-kick clattered to crossbar — the ninth time the Frenchman has hit the woodwork in all competitions this season.
United finally found the back of the net in the 70th minute but Ibrahimovic was marginally offside, saving the blushes of Robles who made a mess of trying to stop the Swede’s header.
The striker was onside in the 89th minute when he seemed to have a better chance but could only plant his header into the Stretford End.
But he was to be given one more chance from the spot and he made no mistake, sending Robles the wrong way.
De Gea 5, Young 6 (Shaw 65), Bailly 6, Rojo 6, Blind 6 (Pogba 46, 6), Carrick 6 (Mkhitaryan 65, 5), Fellaini 5, Lingard 6, Herrera 7, Rashford 5, Ibrahimovic 6.
Romero, Martial, Fosu-Mensah, Darmian.
Robles 6, Baines 7, Jagielka 7, A Williams 6, Holgate 6, Barry 6, Davies 6, Gueye 6, Barkley 6 (Calvert-Lewin 80, 5), Mirallas 6 (Pennington 65, 6), Lukaku 7.
Stekelenburg, E Valencia, Lookman, Kenny, J Williams.