The hosts led when Paul Mullin tucked away a penalty after Nicky Hunt had pulled down Kevin Ellison.
Tom Barkhuizen wasted a good chance to double the home side's advantage when he dragged wide, and Chris Clements capitalised by levelling from close in.
Substitute Yussuf then won it for Mansfield, prodding in from six yards after Lee Collins' shot was saved.
The Stags now move to ninth and within a point of the play-off places, albeit having played four more games than seventh-placed Accrington, while Morecambe stay 14th.
Adi Yussuf struck a last-gasp winner as Mansfield netted twice in the final four minutes to win at Morecambe.