To make matters worse for boss Nick Henry, skipper Neil Bishop was given his marching orders for fighting in the very last minute and will now miss the next three games.
Boro could and should have taken at least a point from the game but they lacked the cutting edge in the final third of the field.
The Seasiders controlled much of the first half, creating the better chances.
Simon Weaver has the best opportunity of the first period, but his powerful header was bundled off the line by Morecambe skipper Jim Bentley.
Within a minute of the restart, Bishop was sent clear of the visiting defence, but his shot was well smothered by Ryan Robinson.
Morecambe did start to come back into the game after this, with a Bentley header bringing the best out of Leigh Walker in the home goal.
With just nine minutes left on the clock, the decisive blow was struck.
Cartlon was given the freedom of the McCain Stadium to run through and slot home under Walker.
Boro nearly hit back immediately as sub Mark Eccles hit a shot that slammed against the post, but Brian Wake fired the rebound over with the Morecambe keep stranded.
The visitors battened down the hatches in the final moments as Scarborough launched attack after attack, but to no avail.