York were the better side in the opening stages but Ryan Burge slammed in his first goal in the Football League before Jennison Myrie-Williams scored from the spot. Jamie Reed made it 2-1 with a low finish before he prodded home from point-blank range.
Vale came to life in stoppage time when Louis Dodds had an effort cleared off the line, but home manager Micky Adams was quick to praise the visitors.
Adams said: "It's disappointing to lose a two-goal lead, but I thought York were excellent from start to finish and we will take the point and move on.
"We struggled to get hold of the ball throughout and when we did get it we gave it away cheaply. It wasn't a good performance.
"I've got a few players who are feeling sorry for themselves and need a bit of loving at the moment. I'll have to put my arm around them even though I feel like strangling them."