Bellamy ran himself into the ground with an excellent performance, looking dangerous in and around the box.
Freddie Ljungberg set up the first goal when he fired in an excellent crossfield ball from the right, and Bobby Zamora met with his head to loop the ball over Flahavan between the Southend sticks.
Zamora was unlucky not to have scored earlier with a header from a free-kick taken by Lucas Neill.
The second goal came as Lee Bowyer flicked on Matty Etherington's free-kick, but the veteran midfielder has still to break his duck for the Hammers, as the ball crashed against the cross bar. Bellamy pounced to mop up the rebound with a nod of his head.
And so West Ham ended a totally dominant first half display 2-0 up.
Five minutes after the break Freddie Ljungberg was involved again when the impressive Zamora snatched a poorly placed back pass and rounded Flahavan to unselfishly let in the advancing Ljungberg, who finished with a slightly deflected strike.
Southend got one back through captain Maher, but West Ham were undoubtably the dominant force today.
Alan Curbishley will be particularly relieved that he has no fresh injury concerns after the game and will be especially encouraged by fine performances from Bellamy, Zamora, Ljungberg and Bowyer.
West Ham: Green; Neill, Ferdinand, Gabbidon, McCartney; Ljungberg (Reid '72), Noble, Bowyer (Mullins '64), Etherington (Pantsil '78); Zamora (Cole '59), Bellamy. Subs unused: Wright, Spector, Upson, Collins, Davenport.