The home side came flying out of the blocks to test the Shrimpers mettle, but found Dan Bentley in top form in the early part of the game.
Those first half saves proved crucial as the game moved into the second forty-five minutes, when a rare John White strike and a cleverly taken goal from David Mooney separated the two sides.
The first chances in the game saw the U's the more potent, with Moncur sliding in Porter, who was denied by Bentley coming out to sweep up at his feet.
Parish pulled off a good save to tip a deflected Mooney effort over the bar, before his opposite number Bentley saved well at the feet of Porter after initially spilling Moncur's shot.
Two minutes later, Moncur had another effort but, after working his feet to get the ball away from the Southend defence, but he scuffed his shot straight at Bentley.
The Shrimpers tested the U's back line when Barrett had two bites of the cherry in the box from a free kick, but the home side cleared their lines.
As the half entered its final fifteen minutes, Southend started to move into the ascendancy.
Elokobi pulled off a fine tackle to rob the goal bound Payne, before the ball then was sent across from left to right, with Harriott on hand to hack away.
The game was all square at the break and boss Kevin Keen would have been happy with what he saw in the opening forty-five.
However, four minutes after the restart and the visitors were ahead.
It was perhaps a somewhat surprising goalscorer, as a corner was cleared out to the feet of former defender John White, who half volleyed into the bottom corner.
Six minutes later, they had the ball in the back of the net again but the passionate celebrations in the away end were cut short as the linesman flagged Mooney offside.
A minute later Ambrose flashed a header wide, before Harriott had a shot deflected behind for a corner.
Next, Ambrose lashed a low volley in from Wynter's cross, but it was well held by Bentley.
And that save proved crucial as Southend doubled their advantage with seventeen minutes left.
Elokobi got caught on the ball by Hunt, who sent Mooney away. Eastman got in, Parish came out, but neither could deny the Irishman as he managed to find space to slot the ball home.
After Moncur had had a shot cleared off the line earlier in the half, he curled another one just past the post and Bentley pushed another shot from Wright away from danger as he continued to repel the U's efforts.
The final whistle blew and it was the Shrimpers who were singing on the final whistle.
The U's will keep on fighting though and, under Kevin Keen, the second half of the season will see them aiming to pull clear of trouble.