Head coach Graham Potter admitted conceding a third goal so soon after reducing the deficit to 2-1 was a killer blow for Brighton at Old Trafford.
It was a below par display from Albion who were well beaten 3-1 by a Manchester United team inspired by sublime performances by Marcus Rashford and Daniel James.
Andreas Pereira opened the scoring in the first half with a shot that deflected off Dale Stephens. The second was an own goal from Davy Propper, after VAR referee Peter Bankes saw nothing wrong with Harry Maguire's elbow to Dunk's cheekbone in the build-up.
Dunk made it 2-1 after the break when he converted a corner from Pascal Gross but Rashford soon struck for 3-1 with a shot that crashed in off the bar.
Potter said, "They deserved to win the game, if you make any mistake they can turn defence into attack so quickly. The players gave their best, but sometimes you have to accept you are playing against a better team. We had a decent period in the league and now we need to get ready for another tough match.
"They key moment for us was when we went 2-1 down despite not being much in the game, if we could have kept that score for longer it could have made a difference but United responded scoring the third goal so early in transition."
Brighton drop down to 11th with 15 points from 12 while Manchester United move up from 10th to seventh.
Their manager Ole Gunnar Solskjaer said, "We should have scored many more goals. It was an excellent performance from the lads, when you see them going forward it is a joy to watch.
"Anthony Martial did not get a goal but he was outstanding. Brandon Williams was excellent too, he has had some good games already and he seems he wants to be out there and enjoy himself.
"The table does not really matter at the moment: we need to keep improving and keep winning games and see where it takes us."
Brighton have played a possession-based style of football under Potter this season and have dominated many matches. But United pressed them continuously and looked to break with pace on the counter attack.
James added, "The high press paid off, that’s what we have been about all season, playing with energy right from the start. We were a little bit edgy when they scored and it was good to score again on the break. But we could have scored also seven or eight goals."
Rashford was excellent throughout but also missed an easy chance in the second half when he fired wide from close range from James' cross.
"Marcus normally scores a lot of those goals," said James. "Thankfully when he missed we were already 3-1 up."
Man United: De Gea, Wan-Bissaka, Lindelof, Maguire, Williams (Rojo 91), McTominay, Fred, Pereira (Lingard, 70) James, Rashford (Greenwood, 91), Martial. Substitutes not used: Romero, Jones, Mata,Garner
Brighton: Ryan, Montoya (March 45), Duffy, Dunk, Burn, Trossard (Gross 59), Pröpper, Stephens, Alzate, Maupay, Connolly (Murray, 45) Substitutes not used: Button, Balogun, Mooy, Schelotto