A second defeat for the Seagulls and a first win for the Youths.
It begins to look like Bray will have to make their exit from the First Division over the long haul, as opposed to running away with it.
Early promise from the Wanderers, with efforts by Philip Gannon, Paul Keegan and Joe Doyle inside the opening ten minutes, gave an impressive travelling support a false sense of security, and as the first half wore on, Bray's initial dominance seemed to fade a little.
Doyle came close to opening the scoring after further half-chances by Gannon and himself, but his touch on a cross from Dylan Barnett was poor, and Lee Costello had little difficulty clearing before it might have trickled over the line.
Minutes later, Wexford thought they had taken the lead when Danny Furlong tapped in Emmet Nugent's cross, but the celebrations were cut short by the offside flag.
Dylan McGlade had the final action before the break as he turned his marker well but his right-foot shot from just outside the area flew narrowly over the bar as the half time whistle sounded.
There was little in the opening action of the second half to hint as what was to follow.
Nine minutes in, Wexford intercepted a Bray clearance, and a long ball into the area was nodded back by Seán Callan to the unmarked Nugent, who volleyed it in a high loop to Sava's left-hand post.
The Seagulls tried to hit back quickly, with Dylan McGlade shooting narrowly wide, and the familiar figure of Hugh Douglas, making his first start in almost a year due to injury, headed just off target a minute later.
The hosts almost grabbed a second just inside the hour, when Darragh O'Connor played a through ball for Furlong, but he dragged his effort wide of the right post.
McGlade had another opportunity, waltzing through the defence, but former Seagull Corey Chambers in the Wexford net managed to turn his close-range effort behind,
And soon after that, a fine run by Seán Callan looked threatening until the visitors' defence managed to scramble his cross clear.
But while the visitors were struggling to find a way back, disaster struck.
Bray took a quick free in midfield which rebounded off Doherty in the centre circle.
He himself was quickest to react and gained a full 10m on the Seagulls' defence as they raced back in an effort to get between him and Gabriel Sava, and from the edge of the area he curled another far-post shot past the stranded keeper.
In the closing minutes, Wanderers tried to salvage something, with Paul Keegan having another go and McGlade seeing his shot in the final minute of regulation time well saved by Chambers.
He was back again in time added, but couldn't keep his last-gasp effort down.
Journeys home without any points always seem longer. At least tonight's was one of the shorter ones.
Compiled by Mícheál Ó hUanacháin
Bray Wanderers: 1 Gabriel Sava; 22 Luke Nolan, 2 Hugh Douglas, 4 Kilian Cantwell, 3 Dylan Barnett; 7 Dean O'Halloran , 10 Dylan McGlade, 6 Paul Keegan (c) , 8 Philip Gannon, 11 Derek Daly, 9 Joe Doyle