Matheus Cunha scored a sensational 87th-minute winner to clinch a 3-2 victory for Michael Carrick's Manchester United and cut Arsenal's lead at the top of the Premier League to four points.
Substitute Cunha curled a stunning finish into the corner from 25 yards out, only three minutes after Mikel Merino had hauled the lacklustre hosts level from a Bukayo Saka corner.
Earlier, Arsenal had squandered a lead when Martin Zubimendi's poor pass allowed Bryan Mbeumo to run through on goal and beat David Raya after Lisandro Martinez had diverted Martin Odegaard's cross-shot into his own net for the opening goal.
Arsenal struggled to regain their composure after Mbeumo's leveller and Manchester United, 2-0 winners over Manchester City in Carrick's first game in charge last weekend, went in front when Patrick Dorgu crashed a superb effort in off the bar.
Mikel Arteta tried to change the flow of the game by making a quadruple substitution before the hour mark, but Arsenal continued to flounder before finally restoring parity when Merino prodded over the line for yet another set-piece goal.
At that point, it seemed Arsenal might go on and find a winner, but Cunha silenced the Emirates Stadium when his stunning, long-range effort sparked more wild Manchester United celebrations. There were boos from some home fans at the final whistle.
The victory continues a dream start in the dugout for head coach Carrick, and leaves alarm bells ringing for Arsenal, whose lead at the top of the Premier League is reduced from seven to four points following Manchester City and Aston Villa's wins.
Having been held to goalless draws against Nottingham Forest and Liverpool in their previous two Premier League games, Arsenal are now without a win in three as Manchester United continue to push for a Champions League finish in fourth.