Wivenhoe had the game's first chance after 10 minutes, but Tyler Kemp through on goal blasted his shot against the crossbar.
In a first-half shy of chances, 'Side would go into half-time ahead thanks to a goal from Kevin Difika on 44 minutes. The
defender glancing home at the near-post from a good free-kick delivery into the box.
It was his first goal for the club too, coming on his 12th appearance.
Wivenhoe started the second-half well with Billy Coe's header forcing 'Side keeper Josh Chebesi into a save.
After a decent spell Wivenhoe equalised on 64 minutes, when Mitch Arthur headed home a Kemp free-kick.
Just as it looked like the game would end level, with six minutes remaining Wivenhoe grabbed the winning goal.
Mitchell Arthur saw his shot saved by Chebesi, but Thomas Ashworth was on hand to slot the rebound home
The result leaves 'Side in 9th in the table, with the win keeping Wivenhoe in 4th place.
'Side are next in action away against championship-hunting Ipswich Wanderers who sit top of the table. That match is on Saturday 16th April.
'Side: Josh Chebesi, Jordan Cornelius, Kevin Difika, Patrick Hoy, Ismael Dahjaoui (Anton Aleexander), Elliot Scott, David Etcheri, Archie Hammond, Umaru Kabia (Ali Rajim), Josh Duyile, Quincy Warner
Subs Not Used: Luca Santarelli, Berkcan Belindir