The Shannonsiders went into the half-time break ahead through Lee-J Lynch but second-half goals from Christy Fagan, Conon Byrne, Jamie McGrath and Graham Kelly sealed the win for Pats.
The home side dominated much of the first 45 minutes but should have gone behind but for the heroics of Freddy Hall. Byrne found space 25 yards out and his fierce effort was tipped over the bar before Hall somehow denied Fagan's flicked header from the resulting corner in the 14th minute.
Four minutes later, Markets Field erupted as Lynch blasted home from the edge of the area to leave Conor O'Malley with no chance to cue wild scenes from the huge home support.
Billy Dennehy hit the post with a header five minutes later as Pats pushed their Premier Division advantage home in the second-half. Dennehy was involved when he crossed for Fagan to tap home at the back post to level the tie and the away side were soon ahead.
Man of the Match Byrne found the net with six minutes remaining and the EA SPORTS Cup was won three minutes from time as Jamie McGrath lifted the ball over Hall to seal the win.
With Limerick pressed forward, Kelly ran the length of the pitch to put the ball into a open net as Pats lift the trophy for consecutive seasons.
St. Patrick's Athletic manager Liam Buckley said: "It was a fantastic final and a great occasion. We're delighted to come out on top of course, it was a difficult game.
"In the first-half, they really pressed us back and I think we were taken by surprise. However, after the break, the players performed brilliantly and got the goals our play deserved.
"It's great that Limerick will be back in the Premier Division next season as it's a great facility down here and we've really been looked after since we came down."
Limerick: Hall, Kelly (Tracy 66), Williams, O'Conor, Lynch, Duggan, Greene, Russell, Kenny (Coughlan 81), Mulhall (O'Flynn 71), O'Connor.
St. Patrick's Athletic: O'Malley, O'Brien, Bermingham, Hoare, Byrne, Fagan (Corcoran 86), Desmond, Kelly, McGrath, Dennehy (Timlin 89), Barker.
Referee: Robert Rogers