The Shrimps suffered their third home defeat of the season as they were undone by the Dons.
Christian Jolly gave the visitors the victory with an 84th minute header from Sam Hatton's as the Shrimps' stuttering home form continued.
The visitors had the better of the opening stages with Rashid Yussuff hitting the post on 14 minutes when he should have scored and Jack Midson coming close to Christian Jolley's left wing cross before the Dons were awarded a 15th minute penalty when Gary McDonald was adjudged to have fouled Like Moore.
Moore stepped up for the kick but saw his effort denied by an excellent save from Barry Roche.
The Shrimps then hit back with Stewart Drummond openign the scoring on 20 minutes with a fine finish from Lawrence Wilson's left wing corner.
The visitors equalised on 35 minutes when their top scorer Jack Midson beat Roche at the near post from the edge of the area.
Wimbledon had the better of the second half possession but faoiled to trouble Roche and it was Morecambe who had the best&nbsp;chance to take the lead when Kevin Ellison was presented with a chance six yards out on 75 minutes but Seb Brown produced a superb&nbsp;save.&nbsp;
Morecambe - Roche: Parrish, Fenton, McCready, Wilson; Drummond, McDonald, Hunter: Ellison, Reid, Jevons. Unused subs: Routledge, Charnock.
Wimbledon - Brown; Hatton, Stuart, McNaughton, Bush; S Moore, Minshull, Yussuff, L Moore, Jolley, Midson. Unused subs: Turner, Jackson, Porter, Johnson, Wellard.