Two Aaron Pressley goals during the match preceded penalty conversions from Christian Tue Jensen, Jaakko Oksanen, Dom Thompson, Pressley and Dru Yearwood, as the young Bees confirmed their second semi-final of the season.
The Brentford B line up featured two members of the first team squad in Dru Yearwood and Dom Thompson who started at Kingsmeadow as the young Bees aimed to seal themselves a second semi-final of the season having already progressed to the same stage in the Middlesex FA Senior Challenge Cup.
As for the home side, they fielded five first team players, which made for an entertaining affair.
It was Wimbledon who perhaps made the stronger start to the game as Dylan Adjei-Hersey had the ball in the net with a clever finish but for the offside flag to rule out the goal.
Brentford B then began to see more of the ball on 20 minutes, and they began to threaten down the right-hand side as Matej Majka drove forwards before slipping the ball back for Yearwood who poked wide of goal.
Pressley would then have his first attempt when Adams did well to cross with his left foot before the forward got on the end of it, but for a good save from Nathan Trott who rushed out to deny him.
Just before the half hour mark the young Bees would go ahead when excellent pressure from Fredrik Hammar saw him force the home side into a defensive error before the ball fell to Pressley who swept a left footed effort home.
Nathan Shepperd would be forced into a smart save moments before half-time when a cross to the far post from the right saw Paul Kalambayi shoot from close range, but credit to the Welshman, who was out quickly to make the stop.
The home side would dominate the opening period after the break, and they almost levelled when Finlay MacNab headed just wide of goal after a dangerous cross on 48 minutes. Shepperd would be called into action again when the ball fell kindly for MacNab to thump a volley at goal, but once again, the young keeper wouldn’t be beaten as he pushed the ball over.
With 20 minutes to go Wimbledon would have the chance to level things when Japhet Sery Larsen tripped a Wimbledon attacker as he darted into the box before substitute Zach Robinson converted the resulting spot kick.
It would get worse five minutes later when the home side would take the lead. An excellent cross in from the left-hand side found MacNab who guided a header into the far corner past Shepperd.
With just four minutes to go the young Bees showed excellent character to wrestle themselves back into the tie as Joe Adams, deployed at right back on the day, crossed low for Pressley to slip the ball home at the near post to make it 2-2.
With the game tied at 90 minutes the young Bees would score all five of their penalties as Robinson put his effort over Shepperd’s goal.
Brentford B will now face Erith Town in the semi-final of the competition with a date and time to be announced in due course.
AFC Wimbledon: Trott, Ogundere, Guinness-Walker, Madelin, Currie, Kalambayi (Robinson, 60) Biler, Adjei-Hersey (Olanyian, 88) Lamy, Roscrow (Frimpong, 60) MacNab Subs not used: CoxBooked:
Brentford B: Shepperd, O'Connor, Thompson, Yearwood, Sery Larsen, Oksanen, Adams, Maghoma (Read, 64), Pressley, Majka (Tsaroulla, 84) Hammar (Tue Jensen, 84)Subs not used: Andersson, Koutsimouka