Rhys Murphy gave the visitors the lead but Saidou Khan hit an instant equaliser two minutes later.
Debutant Luke Croll then turned the scoreline around, finishing from inside the area.
Kabongo Tshimanga came off the bench to add a third before Southend’s Sam Dalby missed an injury-time penalty.
Both sides ended a man down as Calvin Miller and Zak Brunt were sent off.
Here are Liam Norcliffe’s player ratings...
13. Nathan Tyson 7
Replaced Payne with 25 minutes to go. Made an impact off the bench with a couple of bursting runs in behind which gave Southend something else to think about. Photo: Tina Jenner
14. Curtis Weston 6
Back from injury and made the bench. Came on for the last 15. Booked. Photo: Tina Jenner
15. Kabongo Tshimanga 7
Came on for the last 15 minutes and scored within four minutes of entering the pitch. He raced onto Kellermann's pass and finished to make it 3-1. Just the 13 goals for him so far this season. Photo: Tina Jenner