Fulham manager Slavisa Jokanovic said his side were punished for poor first-half finishing but insists he will not change his side's philosophy following only their second away defeat of the season.
Former Fulham stopper David Stockdale made a string of first-half saves to stop the visitors extending their lead after Kevin McDonald's 18th-minute opener.
Strikers Sam Baldock and Glenn Murray both hit exquisite second-half goals to turn the game around and hand victory to the Seagulls.
Defeat for Jokanovic's men means they lost ground on the top six, and the Serbian was critical of his side for not being clinical enough in front of goal and for losing their concentration in the second half.
The Fulham boss said: "It was an ugly afternoon for us. We should be going back to London with some points, but we paid the price for not taking our chances and they were more clinical.
"They punished us very hard. I don't have the sensation that they dominated us in the second half and made so many chances. They made only half chances - the complete opposite of what we made in the first half.
"If you don't score, you need to concentrate defensively and we didn't."
Jokanovic played down a heated exchange between the two benches in the second half after a touchline altercation between Baldock and Stefan Johansen.
"It was nothing special," he added. "Chris Hughton is a nice man and he has a good culture. It was not a problem and you see these things in football.
"What's important here is that we don't change our attacking philosophy, continue to be brave and believe in each other."