Both sides had struggled to create chances in the opening 45 minutes despite Fleetwood dominating proceedings - Ball's penalty claim, rightly waved away by referee David Webb, the closest either side came.
The home side upped the tempo after the break and grabbed the lead following a period of sustained pressure.
Junior Brown found space down the left, his cross drifted onto the head of Ball - his effort turned back across Barry Roche in the Morecambe goal and into the net.
Fleetwood pushed for a second and could have doubled their advantage when substitute Alex Titchiner pumped in a cross from the right - Ball with a diving header which drifted wide.
Brown wasted an even better opportunity in the dying stages, Titchiner with a low cross and with the goal gaping Brown somehow firing over the bar.
Former Fleetwood man Richard Brodie created the visitors' best chance, beating Rob Atkinson but shooting well wide.