The Dons had been beaten in all four previous meetings against Paul Sturrock's side and that looked like becoming five when Southend skipper Sean Clohessy fired the hosts in front from the penalty spot in the 29th minute after Pim Balkestein had handled Kevan Hurst's right wing corner.
But Balkestein made amends for his error just three minutes later when he rose high to head Sammy Moore's corner in to the top left-hand corner of the net from six yards.
After that the Dons dominated proceedings and went in front in the 47th minute when Gary Alexander's right-wing cross picked out former Southend loanee Jack Midson, who headed home at the near post from close range.
The visitors then made sure of their win in the 70th minute when substitute Luke Moore scored with his first touch, sending a low, left-footed shot in to the bottom right-hand corner of the net from 20 yards.
- Sports & Recreation
- Pim Balkestein
- Sean Clohessy
- Kevan Hurst