The impressive Dembele, a £5million summer arrival from AZ Alkmaar, struck his first Barclays Premier League goal with a fine equaliser in the 49th minute.
Hungry: Wolverhampton Wanderers' Jelle Van Damme (left) celebrates scoring the opening goal with teammate Stephen Ward
And he also delivered the match-winning free-kick in the dying moments after Wolves' Christophe Berra had been sent off for picking up two yellow cards.
Jelle van Damme gave Wolves an early lead when he tucked home Kevin Doyle's cross, the first act of a traumatising first half for Fulham capped by the departure of Zamora with what appeared to be a serious ankle injury.
Zamora was brought down by a hard challenge from Karl Henry and although the Wolves skipper won the ball, his victim's right ankle was trapped in the tackle and his leg buckled awkwardly.
The 29-year-old, who won his first England cap last month with more seemingly imminent, thumped the turf in agony and was given oxygen before being carried off the pitch three minutes later.
Henry was on the receiving end of angry tirade from Zamora's team-mate Clint Dempsey but it was a fair, if robust, challenge and the injury was more a result of ill-fortune than malice.
Wolves were berated throughout by home fans angry at their physical approach and their display, which resulted in a flurry of yellow cards in the second half, will be scrutinised.
Big blow: Fulham's Bobby Zamora is carried off injured
But that will be of little consolation to Zamora, who only yesterday signed a new four-year contract that made him Fulham's best-paid player on a reported £50,000 per week.
The deal came with a ringing endorsement from Mark Hughes who underlined the importance to the club, but the Cottagers manager could now be missing his most influential player for some time.
Apart from losing Zamora, Fulham will also feel aggrieved that referee Phil Dowd failed to award two clear penalties, one in each half as Wolves crashed to their first Premier League defeat of the season.
Dowd, who was berated at half-time by an angry Hughes, was a target for home fans all afternoon and his performance is sure to come under the spotlight
The first blunder arrived during the opening exchanges when a poor challenge from Jody Craddock sent the onrushing Simon Davies sprawling, but Dowd refused to give the spot-kick.
For all Fulham's early dominance, a lapse in concentration in the 10th minute enabled Wolves to take the lead.
Doyle, having got the better of Brede Hangeland, played a long cross which right-back John Pantsil allowed to run to an unmarked Van Damme at the far post and the defender stabbed the ball home.
Touchy: Rival managers Mark Hughes (left) and Mick McCarthy (right)
The goal took the wind out of Fulham's sails, all the invention and rapid passing they had shown evaporating as Wolves seized the initiative.
Fulham's problems deepened with the cruel exit of Zamora and they produced little threat for the rest of the half.
Danny Murphy dispatched a free-kick high into the stands and although Wolves were on the defensive, they were coping admirably.
The home fans were incensed by their robust tackling and at the same time criticised Dowd for failing to issue any punishment.
When a leaping Sylvan Ebanks-Blake clattered into Hangeland and Henry then played the dead ball back to his own keeper, the Fulham supporters grew even more irate.
Hughes shared their anger and strode onto the pitch to berate Dowd once the half-time whistle had gone.
Strike one: Mousa Dembele scores Fulham's equaliser
Fired up by the injustice of losing Zamora, Fulham began the second half with gusto and were rewarded with a 49th minute equaliser.
Stephen Kelly produced a cross that Zoltan Gera failed to control but the ball squirted out to Dembele and the new signing dispatched his shot into the bottom-left corner.
Keeper Marcus Hahnemann brought down Davies and Fulham could rightly feel aggrieved not to win a penalty as the American got nowhere near the ball.
Wolves were shown a succession of yellow cards as Dowd finally lost patience and chants of "you're a disgrace to the Premiership" filled Craven Cottage.
Worse was to come as Berra was sent off and Fulham seized the chance to deliver the fatal blow.
The free-kick fell to Dembele, who stepped up and smashed the ball into the bottom right corner to complete his side's comeback.
Late show: Mousa Dembele celebrates scoring the winner
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