The striker, on as a second-half substitute, planted a first-time finish beyond Lee Grant following a mistake from Derby captain Richard Keogh in the 90th minute.
Defender Keogh failed to properly clear Junior Hoilett's cross and the ball fell perfectly to Zamora to fire home and spark delirium among the QPR fans and players, with promotion estimated to net the club around £120million.
Zamora's strike came hugely against the run of play, QPR having hung on for the final half an hour with 10 men after the dismissal of Gary O'Neil for denying a goalscoring opportunity.
The midfielder hauled down Johnny Russell on the edge of the box as the Scot bore down on goal, referee Lee Mason brandishing the red card after consulting his assistant.
It was the second time that Zamora has struck the winner in a Championship play-off final, having netted the crucial goal in West Ham's 1-0 win over Preston in North End in 2005.
For Steve McClaren, it was another nightmare appearance at Wembley following his rain-soaked defeat to Croatia as England coach in the vital UEFA Euro 2008 qualifier.
His opposite number Harry Redknapp, meanwhile, enjoyed yet another Wembley success, having presided over Portsmouth's 2008 FA Cup final win over Cardiff City.
Neither side made any changes from their respective semi-final second-leg victories, with QPR's hero from the win over Wigan Athletic Charlie Austin firing the first meaningful effort on goal in the eighth minute, but his rasping drive from 25 yards was always rising over the crossbar.
Craig Forsyth wasted Derby's first half-chance with 25 minutes gone, heading over from a tight angle after getting on the end of Jamie Ward's left-wing cross.
County felt they should have had a penalty two minutes later when Will Hughes cut inside Richard Dunne and fell to the floor, but Mason waved away the appeals with replays showing minimal contact.
Derby were in the ascendancy, Hughes firing over from the edge of the box in the 31st minute, while Rob Green had to get down low to his left to keep out Ward's dangerous curling free-kick 10 minutes later.
McClaren's men dominated the opening stages of the second period, forcing several corners, but it was QPR and Austin who wasted the clearest opportunity in the 57th minute.
Armand Traore, on as a first-half substitute for Niko Kranjcar, cut the ball back from the byline to the striker, who sidefooted the ball narrowly wide of the right-hand upright from 12 yards.
Three minutes later, QPR were reduced to 10 men when Mason showed O'Neil the red card following a cynical challenge on Russell.
Craig Bryson was introduced for Derby midway through the half and immediately brought a save out of Green, while the former England goalkeeper reacted brilliantly at his near post to deny Chris Martin from close range soon afterwards.
Green was in action again on 75 minutes, parrying Simon Dawkins' effort from 10 yards, with Ward seeing his rebound ricochet off the legs of Martin and behind for a goal-kick.
With the game seemingly destined for extra-time, Zamora capitalised on Keogh's error to spark scenes of jubilation, with Derby players collapsing to the turf at the final whistle.
