The shock win for the Blue Square Premier side set them up for a dream tie with near neighbours Swindon Town.
Goals from Chris Giles and Simon Clist put Forest Green in the comfort zone before Fleetwood's strike three minutes from the end.
Mark Robins' Yorkshire side, fourth in League Two, were always playing second fiddle to the Gloucestershire outfit fifth in the Blue Square Premier.
Home fans booed off their own side but gave the visitors a standing ovation after the convincing win.
Rotherham, who came within six minutes of losing in the first clash but for Chris O'Grady's late equaliser that earned the replay, blew a string of chances before Forest Green struck.
And a slick move from Rotherham saw a super ball from Ryan Taylor send Mark Hudson down the right and when Ryan Robinson parried his cross Stephen Brogan smashed a close-range shot into the sidenetting.
A minute later Rotherham were in a panic at the back and failed to clear as the lower league side turned on the style. Forest Green kept up the pressure and Jamie Pitman whipped in a perfect cross from the right and found centre-back Giles who produced a towering header to put his side in front.
Two minutes later the visitors could have stretched their lead when Clist angled a low shot but Andy Warrington parried.
And just before the break Warrington had to produce another sharp save when a Clist pass sent Fleetwood racing into the area.
But nine minutes into the second half Forest Green were in dreamland after adding a deserved second.
A poor clearance from Rotherham skipper Graham Coughlan put the home side on the back foot. Mark Beesley's cross was sliced by Dale Tonge against his own post and it dropped into the path of Clist, who rammed home a low shot.
And only a point-blank save from Warrington denied Fleetwood his 23rd of the season late on, but he finally struck in the 87th minute.