Forest Green suffered their second defeat in four days but will feel unfortunate not to have got at least a point against Morecambe.
Rovers started off well when Jon Richardson latched on to Neil Grayson's flick-on, but his low effort across the face of goal beat everybody in the box.
Alex Meechan almost grabbed his first goal on his debut return to Forest Green, but although his header from Damon Searle's cross looked to be heading for the left-hand corner of the net, Shrimps defender David Perkins got back to clear off the line.
Richardson was involved again in the 15th minute, but this time he headed wide from John Cant's left-hand corner.
Morecambe took the lead six minutes from half time when Garry Thompson's direct free- kick flew into the top right-hand corner from 30 yards.
Thompson should have grabbed his and Morecambe's second just after the hour after getting through the Rovers defence, but he drilled the ball wide of the right-hand post.
Forest Green had a goal ruled offside 20 minutes from time. Cant's cross found Grayson, whose header looped over the keeper and Meechan was there to put the ball into the net, only for their linesman to raise his flag.
Morecambe grabbed their all-important second on the counter-attack when Danny Carlton raced on to a flick-on and fired the ball beyond Steve Perrin into the back of the net.
Rovers deservedly pulled a goal back eight minutes from time when Martin Foster's ball into the box was dropped by Morecambe keeper Craig Mawson and Grayson put the ball into the back of the empty net.
Despite piling on the pressure late on, Rovers were unable to break through to find the equaliser.