Southend were the first to have a shot on target when Mark Gower tried his luck from 35 yards after six minutes, but saw his shot turned out for a corner by Yeovil keeper Steve Mildenhall.
The Shrimpers shaded the opening stages but failed to threaten Mildenhall's goal until they opened the scoring on 20 minutes out of nothing.
Steve Hammell squared the ball from the left flank to Nicky Bailey and the central midfielder unleashed a 25-yard rocket that gave Mildenhall no chance.
The Glovers offered little threat to Southend keeper Darryl Flahavan, although the Somerset side thought they had got on terms on the stroke of half-time.
Skipper Terry Skiverton headed the ball into the net from close range but his effort was ruled out for offside.
Yeovil started the second half more promisingly and saw Skiverton head just over the bar.
But it was Southend who went closer when former Glovers striker Matt Harrold turned his defender and fired straight at Mildenhall from a Lewis Hunt cross.
Yet the visitors got on terms after 71 minutes with their first shot on target.
Marcus Stewart crossed the ball from the right and his strike partner Owusu stabbed the ball into the net via the foot of the left post from six yards.
The goal perked Yeovil up and to counter Blues boss Steve Tilson handed substitute winger Damian Scannell his debut following his transfer window signing from Blue Square South side Eastleigh.
But the hosts were reduced to ten men when Harrold was sent off for a second bookable offence following a foul on Mildenhall five minutes from time.