Neal Maupay went from hero to villain as his stoppage-time handball gifted Manchester United a penalty which Bruno Fernandes converted to secure a 3-2 victory at the Amex Stadium.
Brighton thought they had snatched a deserved point when Solly March headed home to cancel out Marcus Rashford's brilliant solo goal to level the score at 2-2 in the fifth minute of added time.
But Maupay, whose first-half Panenka penalty was cancelled out by a Lewis Dunk own goal, was adjudged to have blocked Harry Maguire's goal-bound header with his arm at the death.
Maupay's infringement was initially missed by referee Chris Kavanagh, who blew the full-time whistle, but a pitchside VAR review handed Fernandes a penalty of his own which he dispatched into the top corner to seal the unlikeliest of victories for Ole Gunnar Solskjaer's below-par side in the 100th minute.
For Graham Potter, an inquest into how his Brighton side slipped to back-to-back home defeats may point to Maupay but, having hit the woodwork no fewer than five times, the Seagulls' finishing was as culpable as the Frenchman.
Brighton: Ryan (6), Lamptey (7), White (6), Dunk (6), Webster (6), March (7), Alzate (7), Lallana (6), Trossard (8), Connolly (6), Maupay (5).
Subs: Gross (5), Jahanbakhsh (6).
Man Utd: De Gea (7), Wan-Bissaka (6), Lindelof (7), Maguire (6), Shaw (6), Matic (7), Pogba (6), Fernandes (7), Greenwood (6), Martial (6), Rashford (7).
Subs: Fred (6), Bailly (n/a), Van de Beek (n/a).
Man of the Match: Leandro Trossard
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How United beat Brighton in bizarre finale
Brighton were better than Manchester United in every department as the visitors struggles to get to grips with the Seagulls' dangerous formation in a one-sided first half.
Trossard cannoned a left-footed drive off the frame of the United goal inside nine minutes, and the Belgian was denied by the woodwork again midway through the half after exploiting space in front of the visiting defence and getting a shot away.
- Adam Lallana replaced the suspended Yves Bissouma in Brighton’s only change from the win at Newcastle.
- Marcus Rashford, Nemanja Matic and Aaron Wan-Bissaka returned as Man Utd made three changes from the defeat to Crystal Palace.
Brighton were denied by the crossbar on the half-hour mark when Adam Webster's header looped over David de Gea, and the third close call looked to kick United into gear as Mason Greenwood applied a thumping finishing touch to a slick attack, only for the offside flag to chalk the effort off.
But Brighton eventually got the breakthrough they deserved as Maupay's stunning chipped penalty down the centre of the goal punished Bruno Fernandes' rash challenge on the lively Tariq Lamptey in the area.
However, the lead would last just two minutes as United hit back. Fernandes' dipping free-kick was kept alive by Nemanja Matic at the back post and Dunk fired into his own net while under pressure from Maguire.
Brighton looked to have secured the chance to restore their lead within seconds of the restart when Aaron Connolly was bundled to ground in the box by Paul Pogba, but referee Kavanagh found it was the Brighton striker who initiated the contact when reviewing at the pitchside monitor.
Moments later, it was United's turn to be denied by VAR when Rashford's near-post finish was ruled out for offside. But, not to be denied, the United striker gave his side the lead with a stunning solo effort, sitting Seagulls defender Ben White down twice before firing into the top corner.
Brighton peppered the United goal in search of an equaliser as March and Trossard - for the third time - were denied by the woodwork, but the Seagulls' perseverance was rewarded in the final minute of stoppage time when the unmarked March headed substitute Alireza Jahanbakhsh's cross into the unguarded net.
But in a remarkable ending, a melee of players from both teams engulfed referee Kavanagh as he headed to the pitchside monitor for a second look at Maupay's handball.
Despite already blowing the full-time whistle, play was pulled back to award United the penalty and Fernandes held his nerve while others were losing their heads around him to seal United's first win of the season.
Opta stats: Brighton hit post, pay penalty
- Brighton hit the woodwork five times in this game, the most any team has done in a single Premier League game since Opta started recording this data (2003-04).
- Manchester United have won each of the last four Premier League meetings with Brighton, their joint-longest winning streak against a current top-flight side (also 4 v Leicester).
- Since the start of last season, Manchester United's Premier League games have produced 20 penalties, the most of any team in that time (15 for, 5 against).
- Manchester United have given away a penalty in consecutive Premier League games for the first time since March 2009; it's the first time the Red Devils have conceded one in both of their first two games to a Premier League campaign.
What the managers said…
Brighton boss Graham Potter: "I thought we scored with the last kick of the game - I don't know where the extra time came from to be honest. We are bitterly disappointed to concede the way we have; at the time we have.
"We played with real courage and spirit - I'd say we deserved something from the game, I would say that's an understatement.
"We had more chances and shots and hit the woodwork a few times but sometimes football's not fair - I have to accept that, as much as it's painful."
Man Utd manager Ole Gunnar Solskjaer: "I don't think we ever scored after the final whistle, no that's right. But of course their handball was before full-time so it's the probably right thing to do and for us it's a big thing.
"We've discussed it this season - that we need more late goals. We were the team that lost the fewest games apart from Liverpool last season, but we drew too many, and to get two extra points after conceding the equaliser so late on it's a great boost for us.
"We've got to be honest enough to say they created the most chances, they had big chances, so we need to improve a lot going forward."
Brighton host Manchester United again in the fourth round of the Carabao Cup on Wednesday at 7.45pm - live on Sky Sports Football.
Live EFL Cup
The Seagulls then travel to Everton in the Premier League on Saturday at 3pm, before United host Tottenham on Super Sunday at 4.30pm - live on Sky Sports Premier League.