It had a dramatic start when Accrington took the lead after only 30 seconds through Steve Jagielka, who stunned the home defence when he cracked the ball home after a rapid two-man move from the kick-off, catching goalkeeper Leigh Walker and the defence completely off-guard.
A buoyant Accrington continued to have the upper hand with Michael Welch forcing a great header just the wrong side of the post. Scarborough fought to get back into the game with two good chances for Adrian Harper and Mark Quayle, who found the net only to be ruled off-side in a controversial decision.
The Seasiders suffered a major blow when skipper Steve Baker had to be stretchered off with a suspected broken bone in his leg, but despite protests from the home side and the terraces, referee Short refused to send culprit Andy Proctor off, deciding instead to give him a booking.
With feelings still running high, the referee was again at the centre of a dispute when he awarded Accrington a penalty which Peter Cavanagh blasted into the right-hand corner of the net in the 15th minute after Scarborough's Michael Coulson had brought down Ian Craney.
Ian Clark quickly emerged as the best hope for Scarborough to reduce the arrears, master-minding some fine moves. Then seconds before half-time Quayle moved in swiftly to stab a well-placed ball from Harper into the net.
Accrington fought back hard after the re-start and goalkeeper Walker did well to finger-tip a great shot from Craney on to the roof of the net
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Scarborough should have scored through Quayle, but he hesitated under pressure in the goalmouth and was intercepted.
Scarborough had two chances from Ian Clark and Harper, before 17-year-old substitute Jake Speight, on loan from Sheffield United and on work experience, scored his second goal in two days, seizing his chance when Quayle and Clark flicked the ball into the box.
Paul Foot emerged a strong trouper for Scarborough in the later stages, and earned well deserved applause two minutes from time when he headed a spectacular shot from Gary Roberts off the line.
With seconds to go, Accrington's hopes of earning three points were raised when Roberts slipped a neat ball to Andrew Mangan, whose effort hit the woodwork.