The Saints came close to opening the scoring after just four minutes when Graham Kelly saw his shot deflected just wide.
Some desperate defending from Gary Delaney and Stephen Last kept the homeside level and after eight minutes it took a superb save from keeper Graham Doyle who managed to tip a dipping header from Kelly over.
Wexford Youths were unable to gain any sort of possession in midfield where Keith Treacy and Conan Byrne were dominant.
The winner arrived after 26 minutes. Stephen Last was robbed of possession by Ger O’Brien who put in Ian Bermingham with the full-back neatly placing the ball beyond keeper Doyle.
Pat’s, having their first Premier game since July 9, continued to dominate the second-half. Fagan went close and Mark Timlin glanced a header just wide.
Youths in a rare attack saw a Jonny Bonnan effort easily held by keeper Clarke and 13 minutes from time Furlong fired a Conor O’Keeffe cross over.
G Doyle, C McCabe, G Delaney, S Last, L Grace, C Kenny (S Dempsey 82), J Bonner, S Dunne (C O’Keeffe 77), D Furlong, A Mulligan, A Friel (Aidan Keenan 60).
B Clarke, G O’Brien, D Dennehy, S Hoare, I Bermingham, C Byrne, K Treacy, M Timlin (S Kinsella 82), C Fagan, G Kelly (S Verdon 86), B Dennehy.