Despite a battling comeback from Farnborough Town, deadly finishing from Morecambe handed Jim Harvey's play-off hopefuls three points at Cherrywood Road.
After starting strongly Boro were soon on the back foot, due to a series of defensive slip-ups.
Terry McFlynn opened the scoring for the Shrimps in the seventh minute when he volleyed home from inside the area.
The tidy finish came courtesy of good work by his strike partner Danny Carlton who robbed possession from Nick Burton in the Boro defence.
Carlton then doubled the advantage 12 minutes later after a moment of hesitancy from Anthony Charles. McFlynn this time turned provider and his neat throughball was finished clinically as Carlton lobbed the on-rushing Mark Osborn.
The threat did not end there. Both Dean Howell and James Bentley posed problems for the home defence down both flanks.
The two combined to make it 3-0 in the 34th minute as Bentley's cross was superbly volleyed home by Howell after Osborn's kick carried the ball into his path.
Then came the comeback with Richard Hodgson pulling the strings in Boro's midfield.
First, his jinking run into the box resulted in a right-footed shot that found its way inside Craig Mawson's left hand post then, his right-sided corner was headed past his own keeper by Morecambe's David Perkins.
The own goal would have had Boro Manager Vic Searle scratching his head at the break as to how his side could have defended so badly and yet still be in the contest.
Morecambe came out the hungrier looking of the two sides at the start of the second half, although you always felt there was an equaliser in Boro's locker.
With substitute Ali Chaaban posing problems for Morecambe's defence the home side pressed in search of the vital goal. Boro's support were celebrating in the 63rd minute when Howard Forinton's cross was slotted home by Nick Burton, however, the offside flag put paid to them lasting.
As the game began to open up you got the feeling that a goal was just around the corner.
Debutante Dennis Oli should have equalised for Boro with a glancing header, while at the other end Carlton saw a snapshot brilliantly saved by Osborn.
The killer blow came with just eight minutes left when Perkins' run and lay off to substitute Ryan Sugden gave the striker time to shoot low to Osborn's left to make it 4-2 to the visitors.
A play-off place for the Shrimps remains a possibility whilst Boro's fight continues in the bottom three.