The Boynesiders looked on course for another draw when Ryan Brennan equalised in the first minute of time added on at the end, but Alan Byrne was adjudged to have handled the ball in the area 60 seconds later and Killian Brennan fired home the resultant penalty to the delight of the visiting fans.
The hosts had the first chance of the game on two minutes as Ryan Brennan showed no family sentiment in dispossessing his brother before eventually releasing Declan O’Brien and the striker’s ball across the face of goal was just missed by Gavin Brennan.
That was the closest Drogheda were to come as Pat’s dominated.
On five minutes Anto Flood almost benefited from a short back pass from Stephen Quigley to Gabriel Sava, but the keeper managed to avert the danger.
Conan Byrne had two quick chances, but scuffed them both, while David Cassidy was required late on in the first half to head the ball clear from a Kenny Browne headed effort on goal.
Drogheda had their own penalty chance on 71 minutes when Killian Brennan tried to control the ball in his own box, only to see it bounce up and hit his hand, and referee Tom Connolly had no hesitation in pointing to the spot.
Declan O’Brien, however, sent the spot-kick wide of the left-hand post.
The game looked set to be heading for a stalemate until the 81st minute when second-half sub Christy Fagan connected with a Ger O’Brien ball at the back post to give the Dublin side a 1-0 lead.
Drogs thought they had saved themselves with Brennan’s goal, but Killian Brennan had the last word.
Drogheda will now have to pick themselves up for Saturday’s Setanta Cup final against Shamrock Rovers.
DROGHEDA UNITED: Sava; Quigley, Byrne, Prendergast, Grimes; Rusk (Brady 77), Daly, Ryan (Hynes 79), Brennan, Cassidy, Gavin Brennan; O’Brien.
ST PATRICK’S ATHLETIC: Clarke; O’Brien, Kenna, Browne (Price 46), Bermingham; Byrne (Kelly 65), Bolger, Russell, Brennan, Forrester (Fagan 76); Flood.
Referee: Tom Connolly (Dublin).