The Shrimpers created the better of the early chances but found themselves a goal behind after 24 minutes.
Peter Clarke fouled Kyle Perry and from the resulting 20-yard free kick David Mulligan curled the ball over Southend's four-man wall and into the top left-hand corner of Darryl Flahavan's goal.
The hosts continued to fashion the better chances, although Marc Richards created and spurned a couple of chances to extend Vale's lead.
Vale looked set to end the season with a welcome win before James Walker equalised in fortunate circumstances.
Simon Francis' long shot from the right bounced off a diving Joe Anyon, hit Walker and rebounded into the empty net five minutes from time.