In the 31st minute a corner from Brett Johnson found the head of Jamie Smith and he looked destined to score before keeper Steven Drench got a hand to parry it into the path of MacDonald, who forced it over the line at the far post.
Morecambe fought back and almost levelled on 38 minutes when Ged Brannan lofted the ball to Chris Blackburn, whose pass across goal could not be met by Danny Carlton.
Brannan was increasingly influential as Morecambe strode forward and saw his own free-kick fly over the bar on 51 minutes before Craig Holloway turned away a Gary Thompson shot.
On 63 minutes Michael Twiss looked certain to equalise when he got behind the Fleet back line, but he blasted wide with only Holloway to beat.
Despite controlling the latter stages of the game for long stages the Shrimps couldn't break down a hard working Fleet defence which held on for an impressive result against one of the best sides in the league.