The Seagulls managed to hold the Premier League champions back until midway through the first half, before Riyad Mahrez, Phil Foden and Bernardo Silva all found the net for Pep Guardiola's side.
The result sees Brighton sitting in tenth place in the top tier table with five matches left to play, and Graham Potter's men will be looking to finish the season on a high and maintain a mid-table position.
Speaking after the side's loss to the Citizens, Potter gave his verdict on the defeat, and said: "Manchester City played really well tonight and deserved the win.
"I thought we defended well in the first half and had good shape and discipline. We were a bit disappointed with how we were on the ball.
"A few easy passes where we had the opportunity to attack and have the ball we couldn't take. That's a combination of a few things and also the opponent being good defensively. We have to be perfect for us to come here and get anything and in the end we weren't.
"In the end their quality told even though there was a little fortune in how their goals came, the first two especially, you have to say over the 90 minutes they deserved to win."
Take a look at the latest news and transfer stories from the Premier League, as the build-up to the weekend's action continues.
1. Toffees could move for Wolves winger
Everton have been tipped to pursue a summer move for Barcelona man Adama Traore, as they prepare to lose star man Richarlison. Traore joined the Catalan giants on loan last January, but the Toffees could swoop if Barca decide not to make the temporary deal permanent. (Football Insider)
2. Hammers linked with Monaco defender
West Ham United have been linked with a move for AC Monaco defender Benoit Badiashile. The 21-year-old centre-back, who is valued at around £25m, is also believed to be on Serie A giants Juventus’ transfer radar. (Sport Witness)
3. Gunners-linked starlet could leave on the cheap
Arsenal could land Koln starlet Jan Thielmann for a fee of just £12.5m this summer. The Bundesliga youngster has shown glimpses of his talent in the German top tier this season, making eight starts and 18 appearances from the bench. However, the extent of the Gunners’ current interest is unclear. (Sport Witness)
4. Palace eye new midfielder
Crystal Palace are said to be talks with Lens’ over a move for their midfielder Cheick Doucoure. The 22-year-old Mali international is likely to cost around £16m, and his teammate Seko Fofana has described him as “incredibly complete” (HITC)