Goals by Lukas Jutkiewicz and Kristian Pedersen were cancelled out at the Estadio do Bonfim.
It meant that all of the competition games had been drawn, but Vitoria lifted the trophy courtesy of their superior goals scored tally in the post-match penalty shoot-outs.
Blues fell 5-3 on penalties, with Odin Bailey seeing the third kick saved, low to the left.
Craig Gardner, Charlie Lakin and Harlee Dean all netted their spot-kicks and Vitoria were unerring past Connal Trueman.
The night before, Vitoria defeated CD Cova Piedade 5-4 on penalties after a 2-2- draw.
Blues drew 1-1 against Piedade and lost 4-3 on penalties.
Dean captained Blues, who adopted a back three again consisting of the skipper, Marc Roberts and Pedersen.
Blues were put under early pressure by the hosts, with Tomas Azevedo going close in the fourth minute with a flicked header from a corner.
But after finding their feet, Blues took the lead after their first meaningful threatening play.
Steve Seddon pressed high on the left to force possession and Isaac Vassell's belligerence and persistence did the rest.
An initial shot was blocked but Vassell recovered the rebound and burrowed his way to the byline, where he delivered a low cross.
The 'keeper palmed it away and onto a defender and the ball reared up at the back post where Jutkiewicz headed it down firmly behind the line, despite Makaridze's desperate attempt to bat it out.
Trueman then had to be wary to get behind a shot from Mathiola that took a deflection on its way through off Pedersen.
Vitoria levelled things up in the 23rd minute after David Davis was robbed off possession just inside Blues half.
The counter came quickly, with Allef making ground on the right before passing square to Zequinha, whose left foot effort went in via Dean's legs as he slid in, the ball bouncing past Trueman into the corner.
In the 30th minute Dean came to the rescue, somehow getting a low cross from the byline from Allef up and away over the crossbar, when facing his own goal.
The opening came after Vitoria took a quick throw on the right into the space where Seddon, who made a challenge to concede the throw, had been.
Maxime Colin whipped in a low cross from the right that Vassell turned first time at goal from 12 yards, but the attempt didn't carry enough venom to get past Makaridze.
Half-time: Vitoria 1 Blues 1
Lakin was the only change for Blues at the break, going into the forward position just behind, where Mrabti played in the first-half.
Ten minutes into the half, Blues earned a corner when an inswinging free-kick from the left by Gary Gardner was just about kept out by defender, the ball brushing off his chest.
From Lakin's deep flag kick, Gary Gardner rose and thumped a header downward, toward the edge of the six-yard box. As Vitoria's zonally-marking defenders squeezed up trying to catch Blues offside, Pedersen killed the ball in an instant and then swivelled a right-footer into the roof of the net - a smart finish.
Five minutes later Blues almost scored a third goal, from a throw-in on the left. Seddon, who was energetic and vibrant all evening, executed a give-and-go with Lakin, who backheeled him in.
Seddon picked out the oncoming Colin on the right of the area and a goal seemed certain when the Frenchman headed at the target but the 'keeper Makaridze readjusted his direction brilliantly and stuck out his arm to knock the ball away.
The home team responded when Leonardo Chao scooted down the right channel and into the box and crossed dangerously, but the ball came out the other side safely.
Blues were pegged back a second time, in the 69th minute, as they were caught napping from a quickly-taken free-kick.
It appeared Blues were expecting play to be stopped to allow Wes Harding come on, but the ball was chipped forward down the left and Hachadi - who had made a swift diagonal run -drilled it low and hard, on the run, towards the near post.
Trueman got down quickly and parried but the loose ball was despatched into the roof of the net by Chao, from six yards.
As the game entered its climax, Blues strived hard to gain the lead for a third occasion but the deadlock remained.
Roberts made a good block to thwart Hachadi, who turned and shot in the middle of the area.
Blues (3-4-1-2): Trueman, Dean, Roberts, Pedersen, Colin, Davis, Gary Gardner (Bellingham 83), Seddon (Harding 70), Mrabti (Lakin h-t), Vassell (Bailey 74), Jutkiewicz (Craig Gardner 83). Subs not used: Camp, Stockdale, Dacres-Cogley, Redmond, O'Keeffe.