Sam Morsy scored his first of the season and Stuart Tomlinson saved a penalty but it was not enough as Vale lost their second league game in a row by a scoreline of 2-3.
Micky Adams made changes for this game with Ben Williamson earning his first league start, Rob Taylor starting as left wingback and Louis Dodds coming into midfield as Sean Rigg, Doug Loft and Lee Collins all missed out.
And the newlook Vale side started brightly with Williamson striking the woodwork in the opening period.
But Vale conceded a penalty after Stuart Tomlinson appeared to bring down Kieran Djilali in the box. Tomlinson pulled off an excellent save from Luke Moore’s spot-kick but Jack Midson was on hand to drive home the rebound.
Vale were back into it straight after the break when Louis Dodds expertly curled a shot into the corner of the net.
However, Wimbledon took the lead for a second time when Gareth Gwillim scored on the hour break.
Vale were getting increasingly frustrated with some erratic referee decisions and were almost denied an equaliser when sub Sam Morsy’s excellent drive was initially disallowed before the officials decided that the goal would stand.,
Vale then missed a glorious opportunity to take the lead when impressive sub Adam Little delivered a superb cross that left Tom Pope clear just five yards from goal. But Pope embarrassingly mis-kicked with the goal at his mercy.
Vale were left to rue that chance when Wimbledon sub Christian Jolley scored an injury-time winner.
Vale: Tomlinson, Yates, McCombe, Owen, McDonald (Richards, 62), Taylor, Griffith, Roberts (Morsy, 71), Dodds, Williamson (Little, 61), Pope
Subs: Martin, Green