Lisandro Martinez’s own goal put Arsenal ahead at the Emirates Stadium, but Bryan Mbeumo equalised before half-time.
Patrick Dorgu’s brilliant blast gave United the lead after the interval, until Mikel Merino’s late leveller looked to have rescued a point for Arsenal.
In a dramatic finish, Brazilian forward Cunha bagged the winner with an eye-catching drive three minutes from full-time.
It was Arsenal’s first defeat in 13 games in all competitions since losing at Aston Villa in December.
The Gunners lost at home for the first time in 18 matches in all competitions since losing to Bournemouth in May.
Arsenal are now just four points above second-placed Manchester City and third-placed Aston Villa, who both closed the gap with wins against Wolves and Newcastle respectively this weekend.
City boss Pep Guardiola this week called Arsenal the “best team in the world”, but Arsenal’s three-game winless run in the league has breathed new life into the title race.
Arsenal still control their destiny but goalless draws against Liverpool and Nottingham Forest had sparked concerns from their anxious fan-base and this was another alarming result for boss Mikel Arteta.
Arteta has not lifted a trophy since the 2020 FA Cup and Arsenal, who have not won the title in 22 years, face a test of their nerve in the coming weeks after blowing significant leads at the top in previous title races.
United’s first win at the Emirates Stadium since December 2017 continued Michael Carrick’s impressive start to his interim reign.
Former Middlesbrough boss Carrick, hired to temporarily replace the sacked Ruben Amorim, started his tenure with a surprise 2-0 win against Manchester City last weekend.
He has already masterminded victories over the top two to lift United into fourth after Amorim’s turbulent spell in charge.
Arsenal’s relentless early pressure was rewarded in the 29th minute.
It was a shambolic goal for United to concede, starting with Dorgu’s failure to head clear from Piero Hincapie’s cross.
Bukayo Saka pounced and clipped his cross towards Martin Odegaard and although the Arsenal captain miscued his shot, Martinez made a hash of clearing under pressure from Jurrien Timber and the ball bounced in off the United defender’s heel.
Arsenal had not allowed a shot on target in their previous two league games.
Yet if Arsenal’s opener had come gifted-wrapped by United, the Gunners returned the favour with an even more careless blunder in the 37th minute.
Zubimendi’s woefully under-hit back pass was seized on by Mbeumo, who glided around Arsenal keeper David Raya to fire home.
Mbeumo’s ninth goal in all competitions since arriving from Brentford maintained the Cameroon forward’s gradual improvement in his first season with United.
Arsenal had completely lost their momentum and Carrick’s men took full advantage five minutes after the interval.
Bruno Fernandes picked out Dorgu and he took a touch before lashing into the top corner from 20 yards.
Arsenal appealed for handball against Dorgu but VAR allowed the goal to stand as a worried silence descended on the Emirates Stadium.
The 21-year-old’s second goal in successive games vindicated Carrick’s decision to move him from defence into a more attacking role.
To their credit, Arsenal refused to surrender and they snatched an equaliser in the 84th minute.
Once again, it was an Arsenal set-piece that did the damage as Lammens failed to catch Saka’s corner and Merino bundled home from close-range.
However, there was a sting in the tale for Arsenal in the 87th minute.
Fernandes and Kobbie Mainoo teed up Cunha for a superb strike that flashed past Raya from 25 yards.
