Penalty drama sees the U's beat Portsmouth.
Bradford have won the northern section and await the U's in the final of this year's competition.
The U18s had experienced spot kick heart break earlier in the season as they fell out of the FA Cup against Plymouth, but this time - again against south coast opposition in Portsmouth, they kept their calm to get through.
Colchester United's youth team reached the national final of the Youth Alliance Cup on Tuesday night as they grabbed a late equaliser before going on to win on penalties.
It was a frantic start to the game, with chances limited for both sides. A couple of robust challenges from Kent won the U’s the ball on the edge of their own area – and also won applause from the home support.
There were no genuine chances for either side in the first quarter of the game, but there was a serious injury worry for Macauley Bonne, who fell heavily on his ankle with twenty minutes on the clock.
There were four or five minutes of treatment for the front man who had made his first team debut earlier in the season and he was replaced by Patrick O’Shea.
There followed a spell of Pompey pressure as the U’s adjusted to losing their front man – Szmodics going up front and O’Shea dropping into midfield.
The U’s did manage to quell that attacking play and get out and attack themselves. A fizzing Sembie-Ferris cross saw the keeper Searle claw it away from danger and, from the next phase of play, the U’s took the lead.
The ball was crossed in from the left by Pollard and it beat everyone, and Sembie-Ferris kept calm to drill in a low shot that beat Searle at his near post.
Pompey came back and Haunstrup flicked a header wide from a corner, before Horsburgh got to the byline and got a last ditch cross in for Chaplin, whose header forced a good save out of Bransgrove.
And the visitors would think they could have been level at half time. Davis stepped up a cross and Jae Heon missed his header at the far post to level.
The U’s got to the half level, although the visitors had had the better chances in the latter part of the half.
The visitors got the goal that they had been threatening three minutes into the second half. A darting run ended with a lobbed shot over the bar, but the referee adjudged that O’Donoghue had fouled his man.
Chaplin stepped up to take the penalty and blasted into the roof of the net to make it 1-1.
O’Donoghue was booked in that incident and Pompey winger Jae Heon joined him in the book for a lunging tackle on Andrews on the right touchline.
The U’s responded well to going behind, with O’Donoghue embarking forward with a swift one-two into the box, forcing a low save out of the keeper with his feet.
The visitors then took the lead as from a free kick given away on the U’s right, Jae Heon rose highest to flick home a header that beat Bransgrove, despite the keeper getting a hand to it.
The U’s introduced Issa for Brampton on 63 minutes and he was straight into the game as he was slid in by Szmodics and his shot was well saved by Searle.
Szmodics had another chance on 67 minutes as Sembie-Ferris drove forward and beat his full back, but his low shot back across goal went agonisingly wide.
It was all Col U at this point, and they got level on 82 minutes. Sembie-Ferris had been lively down the right and he cut the ball back to Harrison, who drilled home as Issa leapt out of the way.
The U’s had another chance late on in the game as they hit Pompey on the counter attack, Szmodics sliding in Sembie-Ferris, but his effort went over the bar.
Then, at the death, Pompey had a chance as Gill flicked in May’s low cross but it went just past the far upright, before Szmodics got in at the other end to force a fine stop out of Searle.
It didn't look great when the U's missed their first penalty and whilst every penalty taker hit the target, James Bransgrove saved two to see the U's through to the final.
The game finished level after ninety minutes and the game was to go straight to penalties to decide the winner.