After scoring only his second goal for Martin Foyle during midweek, Jeff Smith had the first chance of the game when he struck a left footed shot that looked promising but eventually flew over the bar.
The home crowd held their breath when Kevin Maher's left sided free-kick after eight minutes swung in dangerously for Wayne Gray but his header struck the foot of Mark Goodlad's post.
Vale took the lead after 18 minutes when Michael Husbands' hanging cross from the right was met by Leon Constantine whose floating header found Darryl Flahavan's bottom corner.
Vale should have grabbed a second soon after when Smith's corner from the right swung into Tony Dinning but the newly appointed captain somehow managed to head the ball over.
With the away side's attack beginning to look isolated, Vale pushed even harder with another dangerous Smith corner being glanced wide by former Southend player Constantine in the 33rd minute.
Much of the same followed after the break and after Smith had another chance saved, Gary Mulligan went close in the 50th minute after rocketing a 12-yard shot over the bar.
The Valiants finally doubled their lead in the 55th minute when Smith threaded a perfectly waited ball through to Constantine who crossed low and hard for Husbands to finish from close range.
A triple substitution seemed to give Southend a quick shot in the arm but it was short lived as the home defence remaining composed, keeping the new additions at bay for the moment.
However, Southend struck in the final minute when James Lawson fired the ball into a crowded box finding Jay Smith who duly finished from six yards to keep the fans biting their nails.