The Seasiders could find little reply to Rovers' catalogue of breaks in the first half which saw great chances from Jon Beswetherick, Scott Rendell and Paul Wanless each putting Scarborough keeper Leigh Walker under pressure.
Rovers' manager Gary Owers who spent nearly half an hour in the dressing room with his side after the game, said later he was devastated. "The least we deserved was a draw. But we have no-one to blame but ourselves."
He added "It was frustrating but the players have got to understand that a game lasts 90 minutes. We made Scarborough look bad in the first half, but they stepped up their game in the second half as I believed they would and it paid off.
Scarborough manager Nick Henry admitted that he had "a few harsh words" to say at the interval to his side who for much of the first 45 minutes had been forced to pack their goal as a polished Rovers' side created chance after chance.
"It was a game of two contrasting halves" said Henry. "Rovers were the better side in the first half but we thoroughly deserved to win on our second-half display."
Walker worked hard to prevent Rovers from taking the lead in the early stages, but Scarborough's lacklustre display was transformed in the second half, with Michael Coulson being given his chance as a result of injury problems.
Three of Scarborough's key players, Mark Quayle, Brian Wake and Chris Hughes were missing, which gave 19-year-old Jake Speight a great opportunity to shine which he grasped, to be named man of the match.
Scarborough's goal came when Jon Richardson brought down Speight and Neil Redfearn to drive the spot-kick hard into the corner of the net.
Rovers' game lost pace towards the end, while Scarborough threw everything up front in a bid to secure a second goal in a game which was packed with fast end to end action.
Rovers keeper Ryan Clarke was in fine form as Scarborough found to their cost in the second half.