The young Brighton side, that included two 16-year-olds, upped the ante in the second half, and after Baker-Boaitey had fired a warning shot, the equaliser came seven minutes after the restart.
Brighton had started the second half with renewed intent and equalized when substitute Bailey Smith cut back for Clark to fire in an excellent finish beyond the stranded James Binfield.
The best chance of the night came Albion’s way on 69 minutes when the goalscorer was played through to find himself one on one with the keeper. Having buried his earlier chance, the Culver Road crowd expected the net to bulge but Clark’s effort rolled agonizingly wide of the far post to ensure parity remained.
Binfield punched away a free-kick from Tolaj – who had a goal disallowed for offside - before the Brighton captain’s opposite number nine, Gaskin, flashed a shot wide from distance.
For all their new signings, Littlehampton’s best addition is the retention of talismanic figurehead Joe Benn, whom opted to stay with the West Sussex side despite a host of suitors after his 60 goals last term. Benn began this one on the bench but joined the action early in the second half and almost continued where he had left off, only to see his volley fly narrowly wide in the closing stages.
Then came the dramatic denouement: first, Tolaj swept in on the angle after Baker – Boaitey’s quickly taken free-kick into his path before Jarvis swirling set-piece evaded everyone and found the corner. 2-2 after 90 minutes to set up the shootout from which Shannon’s side settled the silverware.
Development coach Shannon was pleased with his team’s second half showing, but also felt there was room for improvement.
“We didn’t play as well as I know we can in the first half, we had a lot of the ball but didn’t do much with it but we rectified that.
“The second half was much better but having gone ahead so late it was disappointing to not see the game out and concede straight away.
“Having said that, in a way it was a good learning point for us because it showed vulnerability on a set piece against a strong, physical side so it’s something for us to work on.
“Games like this aren’t easy; it was a different type of game than we’re perhaps used to but Littlehampton won the treble last season so we were expecting a tough contest and that’s what we got.
“We had three 16-year-olds out there, Joe (Knight) and Bailey (Smith) did well off the bench, Billie Clark played well and Tolaj looked good up front.
“Overall, good preparation and a good opportunity for a good few of the players to stake their claim for a place in my line up for the game at Selhurst Park on Monday, which will be a great occasion and tough test for us.”