Jay Saunders' 48th minute strike for Margate transformed the game after Forest Green Rovers had dominated a goalless first half.
Saunders half-volleyed past Steve Perrin in the Rovers goal from eight yards after a visiting defender inadvertently headed on a right-wing cross.
Rovers ultimately paid the price for their failure to convert first half supremacy into goals.
Forest Green started the brighter side and peppered the home goal with a number of shots, most of them from long range and of little trouble to Margate keeper Phil Smith.
But on 19 minutes Smith needed to produce a good save to keep out Alex Meechan's shot on the turn from ten yards after a clever header back by Neil Grayson.
Margate's best effort of the half came in added time when Adrian Clarke's rasping shot from the left edge of the penalty area came back of the far post.
Darren Watson thought he had scored when he turned the rebound into the empty net from close range, but the goal was ruled out because he was standing in an offside position.
Once Margate had taken the lead just after the break, through, they really looked like losing it.
Their confidence boosted, they became much more attack minded. Only a superb flying save by Perrin from Graham Porter's fizzing 25-yard volley prevented Margate from doubling their lead, but it was not long before they scored again.
Sam Sodje set up the opportunity with a surging 40-yard run past four men to win a corner. Adrian Clarke produced a good inswinging delivery with his left foot and Jake Leberl met the ball at the near post to head powerfully past Perrin off the underside of the bar.
Rovers' best chance to get back into the game arrived on 73 minutes, but Smith produced a great reflex save to push Meechan's close-range drive over the bar.
Rovers tried hard after this, but never again came close to scoring as Margate clinched a rare and vital win at the Hoverspeed Stadium.