Dean Morgan scored the opener from the spot in the first half but Hughes struck 11 minutes from time to deny Wycombe player/manager Gareth Ainsworth a win on his 600th and final appearance.
Vale should have taken the lead in the 19th minute when Chris Shuker's free-kick fell to Ashley Vincent but he skied the ball over from just six yards.
Wycombe made the breakthrough on the half hour when Vale goalkeeper Chris Neal was called up for holding Morgan in the box.
Morgan took the spot-kick and sent the keeper the wrong way, burying it into the bottom left corner.
Vale hit back and skipper Doug Loft almost leveled at the end of the first half while Kortney Hause headed over in the second for Wycombe.
But Hughes nodded in his 16th of season after coming off the bench before Ainsworth dragged his shot wide when given the chance for a fairytale finish to his career.
Vale were effectively promoted last week thanks to their vastly superior goal difference but this draw confirmed their third-place finish.