Doncaster, whose faint hopes of a promotion play-off place were shattered by the defeat, only had themselves to blame.
Rovers were way below their best but still dictated the pace for most of the game against a poor Plymouth side.
The hosts produced the first opportunity as James Coppinger hit a fierce angled shot which was palmed round the post by goalkeeper David Stockdale.
John Oster volleyed just over the top in the 25th minute and Doncaster had a clear cut shout for a penalty five minutes later when full-back Onismor Bhasera bundled over James chambers in the box, but the referee waved play on.
On loan Arsenal youngster Jay Emmanuel-Thomas twice went close in the second-half with a shot that Stockdale did well to parry before saving his header soon after.
Doncaster made the breakthough in the 58th minute following good work from Dean Shiels.
The ball ran to Coppinger, whose first attempt was blocked, but he volleyed home the rebound in fine style.
Rovers were made to pay for slackness at the back less than ten minutes later when substitute Joe Mason equalised after Neil Sullivan had failed to hold an effort from Damien Johnson.
Doncaster still looked to have the game in their grasp, but Emmanuel-Thomas saw a powerful effort tipped away by Stockdale before Hayter was denied another clear-cut penalty appeal when he was barged over by Karl Duguid.
Doncaster had a chance to snatch victory in the 80th minute when Hayter hit the crossbar following a superb move involving Coppinger and James O'Connor.
But it was the Pilgrims who clinched the points when Bradley Wright-Philips nipped in unmarked to head home a free-kick from Bhasera at the death.