Jodi Jones' late substitution proved pivotal as the City number seven fired the Sky Blues to a dramatic, late win at Roots Hall.
It didn't take long for the first chance of the game to be carved out as it came in the second minute, and fell the way of the home side. It was Dru Yearwood who delivered a cross into the box, which was met by the head of Timothee Dieng, but his header was tame and comfortably collected by Lee Burge.
City were by no means on the back foot following a few half-chances for the home side as they fought back immediately and would feel unlucky to not find themselves ahead.
Tom Davies seemed to have headed the Sky Blues into the lead following a Michael Doyle corner, however, the referee had different ideas as he waved play on after the ball was smashed away from danger.
Leading up to the corner, Jonson Clarke-Harris and Jordy Hiwula linked up well ending up with a shot from the winger deflecting wide.
It took 20 minutes for the deadlock to be broken, and it came via Jordy Hiwula. Hiwula began the attack, latching onto a through ball, beating his marker and earning a corner kick.
Doyle delivered the subsequent corner which was met and headed goalward by Clarke-Harris. The ball may have been going in, but Hiwula was on hand to poke it home from close range to grab himself his first league goal for City.
Ten minutes later the Sky Blues had a great chance to double the lead. The chance came from another set-piece and another great delivery from Doyle. Similar to the goal, the recipient was Clarke-Harris, but his header this time was powered over the bar.
For all of the time spent in their own half, United looked lively on the break and great play between Mantom and Cox set Coker away down the left as the home side were in a promising position. However, the full-back delivered a cross which was easily dealt with by the Sky Blues defence.
The home side began to build up a slight head of steam heading into the break but failed to create any convincing chances as the Sky Blues headed into half-time a goal to the good.
HALF-TIME: Southend United 0 - 1 Sky Blues
Just as in the first half, the Shrimpers were the first team to create a chance in the second half. A cross was floated towards the back post which was knocked down by Theo Robinson for Simon Cox to run on to. Cox fed the ball back to Robinson in the air, but the striker could not muster up an effort on goal.
The home side's attempt was quickly followed by an attack from the Sky Blues as Conor Chaplin played a square ball to Luke Thomas who was in acres of space. The winger entered the box and unleashed a shot from 16-yards out which stung the palms of Mark Oxley as he cleared the effort for a corner kick. The subsequent corner failed to amount to anything.
Dru Yearwood suddenly found a change of gear 10 minutes into the second half as he picked the ball up in the middle of the park and dribbled past three City players. The ball was then played out wide to Harry Bunn who delivered a dangerous, low cross into the box. Thankfully Junior Brown was on hand to intercept and clear the danger.
With 22 minutes left on the clock, the Sky Blues found themselves back on level terms as the introduction of Tom Hopper minutes before paid dividends for the Shrimpers. Hopper was played a ball in behind the defence, and with his left foot, struck the ball underneath Lee Burge from a tight angle.
Immediately from the restart, the Sky Blues had a chance to put themselves back ahead through Clarke-Harris. Unfortunately, as the ball fell to the striker, he couldn't manoeuvre his feet quick enough as he was tackled and the ball was cleared.
With 12 minutes left to play, the home side went down to 10-men following the sending off of Simon Cox for a late challenge on Tom Davies that resulted in his second caution in five minutes.
The Sky Blues almost capitalised on the one-man advantage straight away as Junior Brown was the last to have a stab at the ball as the 'keeper gathered following a flurry of deflections in the United box.
Jordan Shipley's arrival nearly mirrored that of Tom Hopper for the opposition, as Dujon Sterling delivered a delightful cross for the midfielder to head goalward. His header was destined for the back of the net but for Mark Oxley who pulled off an acrobatic save to tip the header over the bar.
However, the most influential substitution of the afternoon was that City's number seven as Jodi Jones received the ball on the right-hand side, cut in, beat his marker and let a low, left-footed shot fly which on its way into the back of the net nutmegged Michael Turner.
There was still time left for the hosts to threaten the Sky Blue goal once more before the final whistle. The corner was delivered as Mark Oxley came up from the back, and after some pinball in the City box, the ball was smashed over by Stephen Hendrie, effectively bringing an end to the game.
FULL-TIME: Southend United 1 - 2 Sky Blues
Sky Blues XI: Burge (GK), Sterling, Willis, Davies, Brown, Doyle (C), Bayliss, Thomas, Hiwula ('76), Chaplin ('84), Clarke-Harris ('89)
Subs: O'Brien (GK), Kelly, Jones ('84), Hyam, Ogogo, Bakayoko ('89), Shipley ('76)
Southend United XI: Oxley (GK), Bwomono, Coker ('46), Turner, Dieng, Cox, Yearwood, Mantom (C)('77), Moore, Robinson ('62), Hendrie
Subs: Bishop (GK), Hopper ('62), McLaughlin, Demetriou ('77), Lennon, McCoulsky, Bunn ('46)
Attendance: 7,775 (996 Sky Blues)
Yellows: Coker '22, Davies '56, Cox '73 '78
Reds: Cox '78
Goals: Hiwula '20, Hopper '68, Jones '90+1