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.