Ince, who replaced Brett Ormerod, needed just six minutes to draw his side level, before firing into the top corner from 20 yards in stoppage time to give Ian Holloway's side the three points.
Rovers, who stay in the bottom three, went ahead through Billy Sharp but were made to pay for missed chances as they slumped to their second successive defeat.
Blackpool, boosted by the return of defender Craig Cathcart, had the opening chance of the game, but Gary Taylor-Fletcher failed to keep his effort down.
Sharp volleyed Giles Barnes' cross over the top of Matt Gilks' bar as the visitors, who were beaten 3-0 by Leeds in their last outing, responded.
Blackpool started to assert themselves but could not test Neil Sullivan in the Doncaster goal as Cathcart failed to direct Stephen Crainey's cross goalwards and Ormerod fired wide from 20 yards.
It was Rovers who took the lead after 27 minutes when Sharp converted Barnes' mis-hit shot from close range.
The visitors almost doubled their lead three minutes later but Kyle Bennett's strike from distance just flew over the crossbar.
The Tangerines did start to show some life towards the latter stages of the opening half, but rarely troubled the Rovers defence as Taylor-Fletcher saw his shot blocked by George Friend.
Blackpool were fortunate not to be 2-0 down three minutes after the interval as Pascal Chimbonda's first-time cross just evaded an out-stretching Sharp.
On-loan Liverpool midfielder Jonjo Shelvey tried to spark the hosts into action, but his 25-yard strike sailed wide.
Doncaster continued to attack and Gilks had to be alert to parry John Oster's strike to safety.
Home boss Holloway made his trademark trio of substitutions after 57 minutes, bringing Kevin Phillips, Callum McManaman and Ince into play.
Those changes worked as the latter drew Blackpool level, curling the ball past Sullivan into the far corner.
Rovers almost restored their one-goal advantage immediately after Ince's leveller, but Gilks was on hand to push Sharp's effort round the post.
Sullivan denied Phillips twice as the Seasiders searched for a winner, while fellow substitute McManaman, signed on loan from Wigan this week, brought the best out of Rovers' veteran shot-stopper.
McManaman's weak effort was saved by Sullivan, but the impressive Ince beat the former Scotland international in the dying moments to ensure Blackpool returned to winning ways following their 4-0 defeat to West Ham on Saturday.