Yankuba Minteh, Kaoru Mitoma and Georginio Rutter all got on the scoresheet as Albion made it three wins in a row, in all competitions – after a run of eight without a victory.
The visitors needed just four minutes to open the scoring with Mitoma breaking free and putting the ball on a plate for Minteh.
Manchester United, who were unbeaten in the previous three games, responded well and levelled through a Bruno Fernandes penalty.
It was a sloppy way to concede for Brighton as goalkeeper Bart Verbruggen’s sloppy pass was cut out by Amad Diallo and landed at the feet of Joshua Zirkzee – who was then brought down by Carlos Baleba.
It was a relatively even first-half but the visitors took complete control after the break.
Joao Pedro thought he had restored the hosts’ lead but it was ruled out for a foul by Jan Paul van Hecke on Diogo Dalot.
It didn’t matter, though, as Mitoma and Minteh combined again with the Japan star, this time, tapping in a simple finish the back post.
The in-form Rutter came on a second-half substitute for Danny Welbeck and he made an immediate impact.
The Frenchman grabbed his fourth goal in three games after Onana fumbled Yasin Ayari’s cross.
That goal effectively ended the game as a contest, as Brighton earned their second win over Manchester United this season and their sixth since May 2022.
The Red Devils have managed just two wins against the Seagulls in that time. Their last win against Brighton at Old Trafford was on February 15, 2022.
Here are our Brighton player ratings:
5. Lewis Dunk - 6
Sloppy at times but also showed great composure, in moments, to take the pressure of his teammates. Mbeumo's first goal went through the Brighton skipper's legs, leaving Verbruggen no chance. Photo: Ash Donelon/Manchester United via Getty Images
6. Maxim De Cuyper - 5
First start since the trip to Bournemouth on September 13. He was subbed off injured after just 24 minutes that day. He's been effective off the bench in recent weeks but really struggled today. Amad gave him a torrid time. Very fortunate not to give a penalty away after a touch-and-go moment with the Ivorian winger. Replaced by Tommy Watson after 59 minutes. Photo: Zohaib Alam - MUFC/Manchester United via Getty Images
7. Yasin Ayari - 5
Hooked on the hour mark after a really sloppy performance. It was uncharacteristic from the Swedish international, who is one of Hurzeler's key men. Photo: Ash Donelon/Manchester United via Getty Images
8. Carlos Baleba - 5
If this was an audition ahead of a potential move to Old Trafford, it didn't go to plan for Baleba. He was outperformed by Casemiro in the middle of the park. Booked for foul on compatriot Mbeumo. Some nice moments but not enough to make a telling impact. Replaced after 59 minutes. Photo: OLI SCARFF/AFP via Getty Images