Three minutes later, Tigers winger Jason Price - returning to the starting line-up after injury - became the first name in referee Mr. Friend's book for a foul, and was shortly followed in by Southend defender David McSweeney.
City were pressing for an equaliser, and came close from two Andy Dawson corners. United keeper Ryan Robinson made a great save from Ben Burgess' near post header, and Stuart Elliott was also denied with the head.
Five minutes before half time Elliott fired the ball low across goal, but Price scooped the ball over with a free shot at the back post.
But that didn't matter when City finally found the net a minute later, with a little help from Robinson. He failed to collect on the side of his area, and Danny Allsopp rolled the ball in for his fifth of the season.
Allsopp then put a first-time shot over from Price's low cross as the sides went in level at half time.
City took the lead 12 minutes into the second half. Mark Warren was booked when Ben Burgess tumbled over his challenge on the edge of the box, and Andy Dawson curled the free kick in for a goal on his home debut.
A good move saw Stuart Elliott shoot wide, but his name was on the scoresheet in the 74th minute when he made it 3-1. The ball was played back to Justin Whittle in his own half, and his long ball towards Robinson was challenged by Elliott. He managed to beat the keeper with his head, and then tapped into the empty net.
Peter Taylor made a couple of precautionary substitutions, bringing off Elliott and Richard Hinds, and Southend got back into the game. They pulled one back via substitute Tes Bramble's head in the 82nd minute, but minutes later were reduced to ten men.
Price was tackled in the corner, but the assistant referee awarded City a throw in when the ball hadn't actually gone out. McSweeney's protest towards the assistant was too strong for the referee's liking, and he was given his second yellow card.
Goalkeeper Robinson had also been lucky to stay on the pitch after it looked like he won a challenge for a ball just outside his area with his arms, but the referee waved play on.
The numerical disadvantage didn't deter the visitors, and although City had chances on the counter attack, Southend pushed forwards and almost stole a point in stoppage time.
Dawson was adjudged to have pushed Bramble over in the box and a penalty was given. Bramble got up to take it but his low spotkick was parried out by Kuipers, and then he made a great reaction from the rebound.
It marked a good home debut in front of 12,545 for the on-loan goalkeeper as he saved the three points at the death, and City move up to 2nd as Southend suffer their 13th straight away defeat.
City line-up (4-4-2): Kuipers; Hinds (Melton), Whittle, Delaney, Dawson; Price, Ashbee, Green, Elliott (Holt); Allsopp, Burgess.
Un-used subs: Musselwhite, Keates, Forrester.