A last-minute winner from Aaron Collins condemned Paul Scholes to his first defeat as Oldham Athletic manager.
Jordan Cranston had given the Shrimps the lead early on as Jose Baxter found an equaliser, but it wouldn’t be enough for Latics as they suffered defeat.
The visitors took the lead within five minutes as Latics failed to clear the initial danger and Zak Mills crossed into Cranston who swept home the opening goal.
Paul Scholes’ men were finding it hard to get a foothold in the game as Cranston had a freekick pushed away by Daniel Iversen.
Iversen had to be at his best minutes later as Piero Mingoia found Carlos Mendes-Gomes whose effort was pushed away by the Dane.
Latics eventually created an opening as Gevaro Nepomuceno put a beautiful cross into Chris O’Grady, but he could only miscue the header wide.
O’Grady then nodded one down to Jose Baxter who would be denied by a fantastic save from Mark Halstead in the Morecambe goal.
Centre backs Peter Clarke and George Edmundson both forced Halstead into saves before goalscorer Cranston wasted a golden opportunity up the other end for Morecambe.
O’Grady forced Halstead into another smart stop early in the second half as Latics looked to pile on the pressure for the equaliser.
In truth the home side didn’t created much until 15 minutes left on the clock when Baxter found the net.
He was picked out well by Johan Branger-Engone from the left-hand side and Baxter rose highest to head home.
Mingoia forced a stunning save from Iversen before substitute Urko Vera was denied by a fingertip save from Halstead.
However, Morecambe would steal the three points right as the game hit 90 minutes when Liam Mandeville turned well in the box before laying it on a plate for Collins to tap home.
Latics must pick themselves up as they face a tough trip to Bury on Saturday.
Attendance 4218 (337 Away)
Iversen, Hunt, Edmundson, Clarke ©, Stott (Dearnley 50’), Branger-Engone, Sylla (Maouche 60’), Missilou, Nepomuceno, Baxter, O’Grady (Vera 72’)
Halstead, Mills, Conlan, Kenyon ©, Old, Bennett (Collins 73’), Ellison (Oates 84’), Sutton, Mendes-Gomes (Mandeville 65’), Mingoia, Cranston