Basildon took the lead after 26 minutes through their player-manager Marcus Bowers, with the score remaining 1-0 to the hosts at half-time.
'Side's general manager Steven Le Sage would have been pleased with his team's response after the break, as on the hour-mark they drew level when Ashley Wackers-Kyriako scored.
The strike was the midfielder's second goal in consecutive games, following his goal against NW London in the Thurlow Nunn League Chsllenge Cup - and his tnird of the season to date.
Both teams made changes from the bench in order to win the game, and it looked like the game would be ending in a 1-1 draw.
However with the last kick of the game, deep in second-half injury time Basildon grabbed the winner through substitute Rhys Fatt.
The defeat leaves 'Side in 16th place in the league table.
'Side are next in action away against Wivenhoe Town on Saturday 10th December. Kick-off for that match is at 3pm.
'Side: Manuel Marques, Jordan Cornelius, Ogunkunle Bandele, Ashley Wackers-Kyriako (James Peagram), Alfie Karby, Elliot Scott, Shaquel Foyewa, Demi Elegushi (Gabriel Addo), Archie Hammond (Jonathan Ogunsanya), Michael James-Akerele, Abikariiim Ali (Gerard Thompson-Shaw)