They went in front after just 5 minutes when Martin Foster's inswinging corner was put into his own net by Bill Edwards, while under pressure from Rovers striker Neil Grayson.
A defensive error almost allowed the visitors to get on level terms when Steve Jenkins slipped inside his own area and Jean Michel Sigere latched on to the loose ball only for his effort to be deflected just wide.
Margate keeper Phil Smith came to his side's rescue in the 24th minute when Adrian Clarke's misplaced pass fell to Kayode Odejayi and his drive needed a full stretch to tip it over the bar.
However, Smith could do nothing though about Rovers' second when Darren Jones' free-kick from his own half found Grayson, whose header looped over Smith who had come off his line.
Forest Green made sure they went in at half time in a more than comfortable position when Grayson's attacking long throw into the penalty area was flicked in to the right-hand corner by Odejayi.
Despite a slow start to the second half Rovers found their fourth goal with Grayson again having a hand in the set-up when his ball sent Alex Meechan racing down the right wing.
His low cross was dummied by Odejayi for Foster to score his first goal in two seasons.
Margate did manage a late consolation seven minutes form time when Simon Beard headed home a corner at the near post.