Doug Loft reached four goals for the season, but it was not enough for the Valiants as they suffered their first defeat of the season.
Micky Adams named another unchanged side but brought back Chris Martin onto the subs bench. Former Valiant Luke Prosser started for the visitors with Jemal Johnson on the bench.
But Vale were stunned as the visitors raced into a 2-0 lead after just ten minutes. Former Valiant Luke Prosser crossed for Mark Phillips to head in on five minutes and then just four minutes later, Liam Dickinson scored from just outside the box.
Vale responded by switching Clayton McDonald to a forward role, but the visitors still continued to make the better chances. And Vale pulled one back when the prolific Doug Loft latched onto a hopeful ball to score on 22 minutes.
The Valiants gained confidence from that goal, but their joy was short-lived when Leonard’s strike went through Tomlinson to put the visitors 3-1 up after just 30 minutes.
Micky Adams made two changes at half-time with Rigg and McDonald being replaced by Haldane and Williamson. And Vale had an immediate chance to reduce the deficit when Owen was hauled down in the box and Vale were awarded a penalty. Doug Loft kept his cool to notch his fourth of the season from the spot.
With the formation changed to 4-4-2 Vale made more of a fight of it in the second-half but still failed to put enough concerted pressure onto the visitors, who held on to claim a rare victory at Vale Park.
Port Vale: Tomlinson, Yates, McDonald, McCombe, Owen, Collins, Loft, Griffith, Roberts, Rigg, Pope
Subs: Martin, Dodds (for Roberts, 70), Haldane (for McDonald 45), Taylor, Williamson (for Rigg, 45)
Southend: Morris. Clohessy, Phillips, Prosser, Leonard, Barker, Grant, Sawyer, Ferdinand, Harris, Dickinson
Subs: Bentley, Bilel (for Dickinson, 76), Hall (for Leonard, 80), Johnson, Sturrock (for Harris, 90)