The Blues though had to play the final half an hour with 10-men after Michael Timlin reacted badly to a high challenge by Scott Shulton, receiving a straight red card from referee Rob Whitton.
New signings Michael Turner and Stephen Hendrie both started for the visitors with fellow signee Michael Kightly coming on at half time, but it was young Dru Yearwood that impressed early on.
And it was Yearwood that had the Blue’s first real chance of the game after he linked well with Cox to run clear, but he could only find the legs of Nathan McDonald with his low effort.
Southend opened the scoring midway through the first half when John White’s cross found last season's top scorer Simon Cox at the far post to nod home beyond McDonald.
Moments later Cox almost doubled Southend’s lead as he saw another header hit the top of the crossbar as the Blues looked to press home their advantage.
With less than five minutes to go in the first-half the home side levelled when Karl Oliyide was found by a far post cross from Ben Wyatt, leaving Oliyide with the simple task of tapping home.
The home side wasn't level for very long, however, as three minutes later Phil Brown’s side restored their lead when Marc-Antoine Fortune calmly slotted the ball into the bottom corner from outside the box just before the break.
Michael Kightly was introduced for the first time since making his return to the Blues at half time and he had a good chance go begging early as he had a free header go straight at the ‘keeper.
With both sides making a number of changes throughout the second half the flow of the game suffered, and the two sides came to blows on the hour mark after Michael Timlin saw red following a late challenge by Scott Shulton.
The challenge and subsequent reaction sparked a brawl between both sets of sides, with Timlin being given his marching orders whilst Shulton received a yellow card.
With the man advantage, Braintree looked the most threatening to score, with Dernell Wynter spurning a number of good chances for the home side to level.
Kightly came close to adding a third for the Blues with two free-kicks, one of which had to be tipped over by McDonald, but the first half goals were enough for Southend to secure the win.
Blues XI: Oxley, White (Kyprianou 72’), Hendrie (Cotton 79’), Yearwood (Bridge 71’), Ferdinand (Demetriou 46’), Turner (Matsuzaka 68’), McGlashan (Kightly 46’), Timlin, Fortune (Trialist 61’), Cox (Robinson 61’), McLaughlin (Klass 68’)
Braintree Town: Karl Oliyide 41’
Southend United: Simon Cox 26’, Marc-Antoine Fortune 44’
Braintree Town: Scott Shulton 60’
Southend United: None
Braintree Town: None
Southend United: Michael Timlin 59’