A poor start by both sides in the opening 15 minutes ended with the visitors surprisingly taking the lead when Kieron Walmsley's low 35-yard free-kick took a deflection to defeat Alan Julian in the Boro goal.
Boro responded with Anthony Elding thundering a shot wide following a short free-kick and strike partner Darryn Stamp heading just wide from Matt Hocking's cross.
Walmsley should have had a second on 34 minutes, but he somehow volleyed well over the bar from inside the six-yard box.
The home side went off to a chorus of boos at the break but they were certainly better on the restart. Manager Graham Westley made two substitutions and they definitely pepped up their attacking play.
Despite this Boro did not really test keeper Ryan Robinson and it was Morecambe who could have gone further ahead through Michael Twiss and sub Gary Thompson.
With Morecambe sitting back Boro were allowed to press forward and Stamp again went close, but his header landed on the roof of the net.
Time was running out for Boro and it was clearly not going to be their night when Dannie Bulman's free-kick in added time saw Barry Laker stab his effort just wide.
In fact Morecambe could have had a second, but Julian denied another sub Danny Carlton with his legs.