Hosts Basildon took the lead through Daryl Cooper on 24 minutes, to end the first-period on top.
'Side equalised a minute after the restart, with midfielder Sam Edwards scoring to make it 1-1.
Substitute Kerkstun MacPherson, who came on for James Holland-Malcolm at half-time, won the game for 'Side on 72 minutes.
'Side: Sam Roach, Aidan Lucas (George Eddon), Jak Mochalski, Paul Wright, Maxwell Amoako, George Lutaaya, Michael Ademiluyi, Sam Edwards (Jason Ajoodha), James Holland Malcolm (Kerkstun MacPherson), David Laird, Jason Fontaine.
Subs not used: Jide Tijani, Fionn Glancy