Defender Kevin Gray scrambled an 86th minute winner as Carlisle battled back from a goal behind.
Neil Redfearn grabbed his sixth goal of the season to put Boro infront after just 11 minutes.
Keeper Matty Glennon fumbled a snap shot from Keith Gilroy and the veteran hot shot pounced on the loose ball to score.
Carlisle had already hit the woodwork - Karl Hawley heading against the post after six minutes - and Boro keeper Leigh Walker palmed a Chris Lumsdon corner onto his bar and over as Carlisle pressed for an equaliser.
Scarborough, though should have been two up in the 40th minute when Kevin Nicholson drilled a long pass down the left for Tony Hackworth to out pace the cover and round Glennon only to steer his shot a foot wide.
Walker pulled off a fine save to beat away a fizzing Hawley drive and pushed out a fierce Peter Murphy shot before the break.
A double save by Walker denied Carlisle 10 minutes into the second half. He could only parry Lumsdon's low drive and when Hawley was first to the rebound the keeper managed to touch his point blank shot round the post.
It was all Carlisle as they penned Boro back and an inspired substitution eventually unlocked the visitors defence.
Kevin Henderson replaced Brendan McGill in the 63rd minute and the striker, making his first appearance since the opening game of the season, struck an unstoppable rocket shot from 25 yards, six minutes later, beating Walker low at his post.
The woodwork denied Carlisle again in the 73rd minute, Simon Grand heading against the post and Scott Kerr cleared off the line from Magno Vieira as Scarborough hung on.
But Carlisle's winner came from their 12th corner - a measure of their domination - when Gray headed in from Peter Murphy's flag kick.