The former England striker was signed on loan from Aston Villa this week and made an immediate impact at the Amex Stadium with the opening goal early in the second half.
However, Brighton’s lead lasted just 10 minutes before Hugo Rodallega struck an equaliser and Lasse Vigan Christensen’s goal then turned the match in Fulham’s favour.
Defeat for the home side was compounded by the last-minute dismissal of Adrian Colunga as Sami Hyypia’s Brighton slipped into the bottom three in the table.
Brighton made a fast start by forcing four corners inside the first two minutes and Bent quickly made his presence felt, with Fulham defender Konstantinos Stafylidis making a decisive intervention.
Veteran Northern Ireland defender Aaron Hughes, retaining his place in Brighton’s starting line-up with Gordon Greer out injured, then put a deflected shot wide before coming to his side’s rescue at the other end.
Hughes kept his cool to make an important clearing header following Shaun Hutchinson’s knock down at the far post.
Brighton stand-in captain Lewis Dunk headed over from an Elliott Bennett corner after Fulham keeper Marcus Bettinelli superbly kept out a Bent header with his leg.
The Seagulls were forced into making a change midway through the first half when Kazenga LuaLua was unable to run off an injury to his left leg and was replaced by Rohan Ince.
Bent went close again for Brighton just before the break, forcing Bettinelli to save with his feet after a neat pass from Colunga.
The Seagulls had a let-off shortly after the interval when Ross McCormack got the better of Dunk, but Rodallega wastefully put the ball wide from a good position.
Bent, making his first league start for seven months, then struck to break the deadlock on 52 minutes.
Spaniard Colunga supplied the perfect pass and 30-year-old Bent beat Bettinelli with a first-time shot which went through the keeper’s legs.
Brighton keeper David Stockdale, who spent six years at Craven Cottage, was called into action when he leapt to confidently hold a deep cross by Jack Grimmer.
But the Seagulls could only hold on to their lead for 10 minutes as Rodallega levelled with a clinical finish, firing home first time into the top of the net after a pass by Christensen.
Brighton were fortunate not to have gone behind soon after when Bryan Ruiz headed a great chance wide at the far post.
And Fulham, who were increasing in confidence, threatened again through a free-kick from McCormack which was flicked over the bar by Dunk.
However, it was Christensen who struck to give Fulham victory with a deflected shot 13 minutes from time after a pass from Ruiz.
Colunga was sent off in added time, collecting his second booking for a needless foul on Fulham captain Scott Parker.
Keeper Bettinelli then swooped to get in ahead of Bent by confidently claiming a low cross from Gary Gardner.