Vale's lack of confidence was obvious in the disjointed opening stages and Darren Purse came to the rescue after a mistake by Liam Chilvers let in Britt Assombalonga.
But Purse was culpable when his trip on Matt Lund, on loan at Southend from Vale's neighbours Stoke, led to the visitors taking the lead from a 19th minute penalty.
Sean Clohessy made no mistake with an unstoppable spot-kick high inside Chris Neal's left-hand post.
Assombalonga threatened twice more against a ponderous Vale defence before extending Southend's advantage in the 31st minute.
The fleet-footed striker turned Purse with ease and struck a right-foot shot from 14 yards which took a big deflection off Anthony Griffith to leave Chris Neal without a hope.
It was almost three with the last kick of the first-half when Ryan Leonard's 25-yard shot crashed against the crossbar before Vale were booed from the field.
Vale boss Micky Adams hauled off Purse and Jennison Myrie-Williams at half-time, but the signs of improvement were initially negligible.
Birchall finally landed Vale's first blow on target in the 63rd minute before Lee Hughes gave the home side a lifeline just a minute later.
Chris Shuker flighted over a cross from the right and Hughes' glancing header from 10 yards sent the ball just inside Paul Smith's right-hand post.
Smith later denied Hughes an equaliser with a fine save, but Southend held firm for a deserved victory.