Trailing 1-0 at half time at a rain-swept Carlisle Grounds, the Seagulls’ netted off two corners to extend their unbeaten run to nine matches and climb above their opponents.
Having beaten the Richmond Park outfit twice this season, Wanderers equalised in the 57th minute.
Kevin Lynch’s corner was flicked on by ex-Saint Conor Kenna with Ger Pender wheeling away as to claim the final touch close in, but the ball seemed to go in off an away player.
Alan McNally’s first goal of the 2016 campaign then left the visitors’ Europa League hopes hanging by a thread.
He connected with Lynch’s 70 minute corner. The effort was blocked on the line but the veteran defender headed in the rebound. Jamie McGrath’s first top-flight goal since last May put the Dubliner’s ahead.
In a 12th minute move started by left-back Ian Bermingham, the ball was cross-field with Ger Brien finding Conan Byrne. He got to the right by-line and hung up a cross which was met by Jamie McGrath. Peter Cherrie looked at have the header covered but could only parry the ball over his line.
The visitors almost doubled that lead just before half time. In a 42st minute break, Billy Dennehy squared inside to the unmarked Christy Fagan.
The striker managed to force the ball past Cherrie but Dylan Connolly got back to clear the ball.
Cherrie; Douglas, Kenna, McNally, Lynch; Marks (McDonagh 90 +3), Sullivan, Noone, Connolly (Kehoe 83); Pender (Dean Kelly 78).
Clarke; O’Brien, Darren Dennehy, Barker, Bermingham; Byrne, Desmond, Graham Kelly (Cawley 80), Billy Dennehy (Kinsella 82); McGrath (Corcoran 86), Fagan.
David McKeon (Dublin).