Southend United U23s were beaten 3-1 by Scunthorpe United after two goals in stoppage-time sealed the visitors' place in the Premier League Cup group stages.
Craig Fagan's side put up a good fight in the second half having gone behind very early on in the contest.
Matt Rush equalised in the 66th minute, but a couple of goals for the Iron from 31-year-old Adam Hammill in the 14 minutes of added time at the end of the second-half, which came mostly from a long stoppage following a head injury to Emile Acquah and then another delay after injury to O'Shane Stewart, won it.
And that sent Scunthorpe into a group alongside West Brom, Newcastle United and Hull City.
It was Scunthorpe that started the brighter and they went in front after two minutes with a brilliantly taken goal from John McAtee. The striker took one touch to set the ball up and then another to loop an acrobatic effort over Harry Seaden and into the far corner of the net.
Blues carved open a good chance shortly after going behind when Acquah played the ball wide to the right-hand side for Egbri whose cross found Clifford, but the left-back’s header went over the crossbar.
The visitors were pressing for a second goal and they went close on a couple of occasions, firstly via Reon Potts who turned on the edge of the area and hit an effort wide before Hammill should have doubled the Iron’s advantage, but Seaden was equal to his low shot, saving with his right boot.
Blues’ best chance of the half came on the half-hour mark when a corner to the back post found Mitchell-Nelson, he sent the ball back into the box for Acquah whose header from close range was deflected behind.
It remained 1-0 to the visitors at the break, but only after McAtee missed the target after running half the length of the pitch and then Rush, with another headed chance, hit the woodwork for Blues.
There was a long stoppage in play shortly after the restart following a head injury to Acquah who received treatment for almost 10 minutes before being stretchered off the field in a neck brace.
Replacing the striker was the fit-again Jon Benton, recently back from a broken foot, and it was the 18-year-old who was at the heart of the equaliser.
Benton played the ball out to Kinali who cut inside from the left wing and played a reverse pass down the line for Benton. He got to the by-line and delivered into the box where Rush squeezed the ball beyond the Scunthorpe goalkeeper Tom Collins from close range to make it 1-1.
Blues were on top and looking to get a second which they nearly had when Kinali cut in from the left wing again and almost found the top corner but a deflection took it just wide.
Benton then had a shot from 20 yards out pushed away by Collins before going close again in injury time, of which there were 14 minutes, cutting back on the edge of the area but sending his shot over.
It was an impressive substitute appearance from Benton who was at the heart of a lot of the good work from Fagan's side in the second half.
Blues had a great chance to win it when Egbri's shot was then prodded wide by Rush from 10 yards out, but in the sixth minute of added time Scunthorpe went up the other end and found a winner through former Barnsley man Hammill who slotted past Seaden.
They then made sure of the win from the penalty spot when Richard Taylor fouled Harry Jessop in the box and Hammill converted from 12-yards out, sending Seaden the wrong way.
Blues XI: Seaden, Howard, Clifford, Pianim, Taylor, Mitchell-Nelson, Egbri, Stewart, (Eastwood), Acquah (Benton), Rush, Kinali.
Subs not used: Grossart, Unwin, Osimeh,