An early Cole Palmer goal was cancelled out by Georginio Rutter and Kaoru Mitoma of the Seagulls to help them advance into the next round.
After suffering a 7-0 defeat at the hands of Nottingham Forest last weekend, Chelsea seemed like a big test for Brighton, but Fabian Hurzeler's men did an exceptional job to turn things around and take the win on the night against Enzo Maresca's side.
The Blues had a lucky start to the game as Cole Palmer's volley in the fourth minute was completely fumbled by Bart Verbruggen - who completely misjudged it, leading it to cross the line
However, the Seagulls were relentless in their approach after conceding and did not take too long to equalise through Gerogino Rutter, who headed home the cross by Joel Veltman in the 12th minute.
Chelsea, who had a good start to the game looked flat after conceding and failed to create any chance apart from a looping ball from Christopher Nkunku to Cole Palmer, who headed the ball over the post.
With scores at 1-1, it was looking like this FA Cup game had all the signs of being another goal feast between the two teams as the last time the two sides met, the fixture saw six goals.
However, the game had nothing to it until Brighton finally found the second goal through Mitoma in the 57th minute, who controlled the ball from Rutter brilliantly and finished well to give the Seagulls an upper hand in the game.
Chelsea had an uphill task at hand as they were searching for a goal to keep themselves in the game, but the visitors showed no intent.
Enzo Fernandez was brought in right after the goal, but he was not able to add anything significant to get Chelsea back.
Marseca decided to bring in Tyrique George and Noni Madueke in the 75th minute, but the Brighton full-backs did well to contain the duo.
Defeat means the Blues will now only feature in Premier League and Conference League competition this season.