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:
13. Tommy Watson - 7
Really lively off the bench. His pass led to the free-kick, which Welbeck scored. Some lovely touches. He deserves a start sooner or later. Photo: Mike Hewitt/Getty Images
14. Diego Gomez - 7
Thankfully his injuries were not too bad and he came on to help his team on the hour mark. Really lively and helped Brighton in their late resurgence. Photo: OLI SCARFF/AFP via Getty Images
15. James Milner - 7
Brighton's set pieces were mostly poor but on stepped the veteran who showed how it's done. Well taken corner headed in by Kostoulas at the front post. Milner did well to steady the ship and keep things simple. Photo: OLI SCARFF/AFP via Getty Images
16. Charalampos Kostoulas - 8
We've barely seen him in a Brighton shirt but this goal will do him the world of good. Fine header. The youngster protects the ball well when he has it. Photo: Shaun Botterill/Getty Images