Despite being down to ten men for 55 minutes after Alex Gilbey's red card in the first half, the U's held firm for much of the second half and even had a number of chances of their own.
But, with the first goal of the game always likely to prove crucial, it was former Colchester midfielder Anthony Wordsworth who broke the deadlock and, as the U's pressed for an equaliser, the Shrimpers were able to extend teir advantage.
So bragging rights remain in the south of the county and the U's know they need to make the most of two home games next week to try and close the gap on the teams above.
The scoreline was perhaps not indicative of a game that had been on a knife edge for 80-odd minutes, but the Shrimpers were clinical in the end to kill off the U's hopes of a result.
And, deep into injury time, it was three. The U’s were pressing for a goal, but Southend escaped on the counter attack and although Payne was denied by Brindley, McQueen swept home.
But it was two with two minutes to go, as Barrett flashed a header home to double the home side’s advantage.
The U’s made their final change shortly after the goal, with Briggs making way for Lee as the visitors sought an equaliser.
The U’s defensive discipline had served them well during the game, but they could do nothing about it when Wordsworth got a shot off on 82 minutes, which buried in the bottom corner.
Three minutes later, Kent extended a leg to deny Barnett who looked like he might be in on goals and, despite protestations from the home support, no penalty was given by the ref who was happy the U’s man got the ball.
The U’s had had a good spell, and introduced Ambrose for the final fifteen minutes with the game on a knife edge.
From the resultant corner, the ball found Elokobi at the far post and his lashed effort skimmed the roof of the net.
McQueen was Southend’s main threat and headed wide from a good position on 62 minutes, before Porter saw an effort deflected just wide of goal as the U’s escaped on the counter attack after winning the ball in midfield.
The U’s were defending in two banks of four to protect Parish, but had a good spell of pressure around the hour mark, with Moncur’s shot deflected over the bar by Bolger as the visitors pressed.
He could only watch on as McQueen delivered a dangerous one for Barnet to put just wide of Parish’s near post.
The second half resumed in similar fashion to the first, with the U’s then making their first change seven minutes into the half with Briggs coming on for Massey.
Although the U’s finished the half the stronger, it was all square at the break.
Late in the first half, though, a Moncur free kick found Elokobi at the near post and his effort was only inches wide.
McQueen then fired wide, as the Shrimpers looked to make the most of their man advantage.
Gilbey and Leonard went in for a loose ball and having seen the U’s man’s challenge, the referee didn’t hesitate to show a red card.
The U’s went close on 35 minutes as Brindley’s cross was tipped onto the bar by Bentley, but a minute later the game changed in the home team’s favour.
Porter’s aerial prowess was important for the U’s and, just after the half hour mark, he knocked one down for Massey eight yards out. He managed to spin and get his shot off, but Thompson was on hand to block.
They followed that up with an effort from Payne, but again the U’s were out quickly to block, this time Eastman the man to put his body on the line.
The home side were starting to see more of the ball and McQueen cut in from the right to strike in a shot that three U’s players came out to block.
The U’s responded in kind and, although Edwards miscued his shot, it fell to Garvan, whose left footed effort was well saved by Bentley.
At the other end, though, a long throw found Hendrie at the far post, and his shot on the turn clipped the outside of the post.
The U’s started the game the stronger, and twice the ball almost dropped for Porter in a dangerous area, only for Southend to clear their lines in the nick of time.
The match started in keenly contested fashion, with some strong tackles. One challenge from Thompson on Moncur was too strong for the referee’s liking and he became the first player booked on the day.