However, Mark Rawle showed the way with a tap-in 10 minutes before half time. The City defence failed to deal with a cross and Rawle found the net at the back post.
Mark Greaves had City's best chance of the half, heading David Beresford's cross wide when he should have hit the target.
Musselwhite saved well from Hutchings early in the second half, but the Southend midfielder soon had revenge when he made it 2-0 from the penalty spot. Matthew Wicks brought down Bramble just
Minutes later, Bramble missed from close range before thumping the post, and City were lucky to be keeping the score down to two.
Mike Edwards went off with a groin strain and David Beresford was also replaced as Richard Sneekes and Theo Whitmore came off the bench to try and turn things in the last 10 minutes, but the Shrimpers held on for a 2-0 win.
Starting line-up (4-4-2): Musselwhite; Edwards (Sneekes), Mohan, Holt; Williams, Johnsson, Greaves, Beresford (Whitmore); Alexander, Dudfield.
Un-used subs: Glennon, Van Blerk, Rowe.