Danny Wilson's men are seven points adrift of 20th position and, with only two home matches remaining, they look as good as doomed.
The Dons had their fair share of the early possession, but it was Vale who carried the greater threat with Nathan Lowndes the pivot.
Michael Cummins forced a fine save from Matt Baker and Sam Togwell belted a 30-yard shot against a post before Leon Constantine opened the scoring in the 13th minute.
Lowndes nodded the ball into his path and Constantine placed a delightful lob over Baker from 20 yards for his 11th goal of the season.
Dons levelled in the 27th minute when Dean Lewington crossed from the left and Clive Platt buried a downward header inside Mark Goodlad's left-hand post.
But the visitors were understandably up in arms ten minutes before the interval when a penalty was awarded against Craig Morgan for what appeared a fair challenge on Lowndes.
Lowndes limped off, Constantine sent Baker the wrong way from the spot and, mysteriously considering he was the last defender, no action was taken against Morgan.
There was no controversy about Vale's third goal in first-half stoppage time, however, as Cummins rifled in a first-time shot after excellent work by Danny Sonner and Chris Birchall.
The second period was dull by comparison, although Birchall will feel gutted when a linesman's flag ruled out what would have been a contender for goal of the season.
Dons, to their credit, defended much better in the second half and almost reduced the arrears when Filipe Morais drew a brilliant save from Goodlad just before the hour.