Reds are out of the Johnstone’s Paint Trophy after Southend’s superior finishing earned the League One side a place in the third round.
Myles Weston and a heavily deflected strike from Joe Pigott beat Callum Preston but the home side improved markedly in the second half. Gary Deegan nearly put through his own goal and substitute Shamir Fenelon twice went close before Pigott got his second with three minutes to go.
The home goal drought extended to a fifth game, a statistic Reds will be desperate to improve on Saturday when we return to league action against Leyton Orient.
Mark Yates made six changes for Reds. Joe McNerney returned after injury, there was a debut in goal for Preston and recalls for Simon Walton, Luke Rooney, Lee Barnard and Roarie Deacon.
The visitors included midfielder Anthony Wordsworth, who had a productive loan spell with Reds last season, and he forced Preston into an excellent early save when the keeper touched round his post from the edge of the box.
His evening took a turn for the worse moments later when he was booked for bringing down Gwion Edwards but Southend continued to dominate the early stages. Weston cut inside on 17 minutes and Preston was at full stretch to acrobatically turn his curling effort round the post. From the corner, Wordsworth’s volley from the edge of the box was just wide of the left-hand post.
Reds responded and nearly broke the deadlock three minutes later. Edwards intercepted a stray pass, ran at the Shrimpers’ defence and his cross found Luke Rooney, whose shot took a deflection but goalkeeper Dan Bentley adjusted his position in time to save.
The pace of Weston was a problem for Reds and he opened the scoring in the 26th minute, latching onto Wordsworth’s pass as the home side appealed for offside and applying a confident finish from 15 yards.
Deacon headed well wide from Jimmy Smith’s cross but Southend doubled their lead on 33 minutes. Pigott cut inside from the left and his shot beat Preston with the aid of a massive deflection off Walton which gave Preston no chance of keeping the ball out.
Barnard wasn’t far away with a shot on the turn in stoppage time but the visitors were well worth their half-time advantage.
Lewis Young came on for Liam Donnelly at the break and straight away his cross found Barnard, who bundled the ball home only to be denied by the assistant’s flag for offside.
Reds made a second change on 55 minutes with Shamir Fenelon coming on for Rooney and he nearly made the perfect introduction but couldn’t get a decisive touch to Edwards’ cross. As it was, a Deegan nearly prodded the loose ball into his own net and it needed a goal-line clearance from Ben Coker to prevent Reds reducing the deficit. Fenelon then worked a yard of space but his shot was straight at Bentley.
The hosts were enjoying their best spell of the game, having got control of midfield and using the width offered by Young and Edwards at every opportunity.
Gavin Tomlin replaced Barnard with 20 minutes to go and made his long-awaited return from injury moments after Young had wasted a great chance from a free kick inside the D that he lifted well over the bar.
Deacon then forced Bentley to save a shot that lacked power but the goal Reds’ second-half performance deserved continued to elude them although there was no lack of effort or commitment from Yates’s team in the second half.
They kept going and enjoyed a couple of late corners and it was harsh in the extreme when Pigott beat the offside trap with two minutes to go and lashed an angled drive past Preston that went in off the underside of the bar.