Seapatrick held the upper hand before the break as St Mary’s struggled to settle.
The hosts moved in front but St Mark’s sparked into life after the break.
Ciaran Rooney found Ruairi Feeney, with the later skipping past three tackles before his cross was converted by Ryan Lawless.
Player/manager Conor Hagan fired home the decisive second with a deflected half-volley hit.
ST MARY’S: Danny Devine, Aidan McGrath, Gerard Kerr, Marc Davison, Ryan McKee, Ciaran Rooney, Dermot Kelly, Conor Hagan, Brendan Hagan, Ruairi Feeney, Sean Brady. Subs: Ryan Lawless, Ryan Creaney, Patrick Lamph.