After a win at Stamford bridge in their last match which ended their three successive defeats, while United were struggling to comeback from their humiliating 4-0 loss at Anfield.
Nuno Tavares put Arsenal in front after only three minutes following errors from Raphael Varane and Alex Telles, the defender turning in a simple finish after David de Gea saved Bukayo Saka's shot.Eddie Nketiah then had an effort ruled out by the video assistant referee for offside but after being called to look at his pitchside monitor the referee awarded a penalty for a foul by Telles on Saka immediately before Nketiah's shot, and Saka converted from the spot.
While Arsenal had a good force of attack, United were looking a real danger in attack. The return of Cristiano Ronaldo saw him scoring his 100th Premier league goal, after which Fernandes missed an opportunity from the spot.
While Manchester United's performance bore no resemblance to the embarrassing capitulation at Liverpool, the end result was still the same and their hopes of taking a place in next season's Champions League are fading fast.
They are now six points behind Arsenal, having played a game more and with only four league matches left.
Interim manager Ralf Rangnick has become increasingly outspoken about their failings, likening what needs to be done at Old Trafford under new manager Erik ten Hag to “open heart surgery”
He did some changes here, dropping Harry Maguire after a traumatic week in which the United captain not only suffered a nightmare display at Liverpool but also had to cope with police conducting a sweep of his home after a bomb threat.
It did not have the desired result as United were let down by defensive form on the pitch despite a performance that contained real menace going forward.
United were also left complaining bitterly when they were not awarded a first-half penalty after Cedric Soares appeared to handle. Dalot twice struck the woodwork and Ramsdale was called into action often, so the commitment could not be questioned here.
There was much that was good about United's display but the decisive moment was that second-half miss by Fernandes on spot with Arsenal hanging on desperately at 2-1.
He went through an elaborate talk before carelessly rolling his spot-kick against the post. In that moment Arsenal were reprieved and United struggling, before Xhaka finished them off with a smooth finish against De Gea.
Arsenal winning through adversity
Arsenal’s win saw them getting a superb response after a three league game defeats.
Tavares gave them the perfect start and while goalkeeper Aaron Ramsdale had a mixed afternoon, he also made some crucial saves, one from Telles early on and another from Diogo Dalot proving significant.
But Xhaka's thumping drive gave De Gea no chance and there was a real mood of celebration inside Emirates Stadium at the final whistle.
Arsenal have inflicted serious damage on any slim hopes United may have had of reaching the top four while maintaining the pressure on north London rivals Tottenham in the battle to qualify for next season's Champions League.