But the Valiants were forced to weather a late storm that saw Wayne Gray hand the hosts a lifeline.
The visitors took the game to Southend in the first half with Tony Dinning twice trying his luck, his second shot on eight minutes forcing a fine diving save out of Darryl Flahavan.
Their approach play was rewarded in the 12th minute when Michael Cummins' cross was laid off by Billy Paynter to Lowndes whose low shot beat Flahavan's dive.
Flahavan then tipped over a Danny Sonner effort but had to watch as his team-mates struggled to create any real chances.
The Shrimpers' troubles increased on 28 minutes when Mark Innes picked out Cummins on the left wing. He beat right-back Duncan Jupp and crossed for Lowndes to fire across Flahavan for his second goal.
Blues boss Steve Tilson's half-time teamtalk must have worked wonders because Southend started the second period more brightly.
But the visitors were happy to defend and nearly increased their lead on the hour when Lowndes squandered the chance to complete his hat-trick, firing over Mickey Bell's centre from six yards out.
That let off and the introduction of Mark Gower boosted Southend who saw the winger's header force a good save out of Vale keeper Mark Goodlad on 70 minutes.
Two minutes later, Gower's one-two with Gray ended with the striker's spectacular overhead kick finally finding the back of the Valiants' net.
Freddy Eastwood and Mark Bentley tried their luck as the Shrimpers piled on the pressure and Gray could have got an injury time equaliser but Goodlad was alert to his 10-yard shot and blocked it.