Saman Ghoddos got the all-important goal in style with a fantastic strike from distance in the first half and Luke Daniels saved a penalty in the second period.
The game began with a slightly cagey first 10 minutes at London Colney, the first real chance came from a Brentford B corner where Aaron Pressley, fresh from his First Team debut earlier in the week, rose but was unable to guide his header on target under significant pressure.
The Bees were dealt a blow after just 15 minutes when Julien Carre was stretchered off after going down injured as Joe Adams came on to replace him.
As the half developed Brentford B began to see more of the ball and Ghoddos was orchestrating much of the good play, with the likes of Dom Thompson also involved from Thomas Frank’s side, and the goal came about in style just after the half hour mark.
He received the ball out wide on the left-hand side before driving across the box and unleashing a sensational strike into the top corner of the goal as the side took a deserved lead.
Another chance came for Brentford B just before the break when Ghoddos drove forward from a central position before feeding the ball into Pressley. The Scot held the ball up well before laying it off to Alex Gilbert who fired at goal but his attempt was well saved by the Arsenal keeper.
The Bees started the second period well, and they should perhaps have doubled their lead on 53 minutes when the high press caught The Gunners out and Gilbert fed Pressley who looked to curl the ball home just inside the box from the left-hand side but he could only find the post as Arsenal cleared the rebound.
The hosts then began to see more of the ball, but credit to Brentford whose defensive shape didn’t allow their opponents time or space in behind as The Gunners perhaps tried to force things to no success.
They were given a golden chance to get back into the game on 67 minutes when good play down the right saw Lewis Gordon trip his man before Daniels was on hand to save the penalty down to his right to keep it at 1-0.
Brentford B continued to keep their opponents at arms length, and created another good opportunity going into the closing stages of the game when Gordon cut into the box with quick feet before firing across goal, but the onrushing substitute Lachlan Brook was unable to get on the end of it.
Late pressure in the dying moments came Brentford’s way when Arsenal began to put the ball into the box from a couple of free-kicks, the more dangerous of the two saw Daniels tip behind as the match finished 1-0.
Brentford B: Daniels, Thompson (Gordon, 45), O’Connor, Hammar , Pressley (Valgeirsson, 62) Gilbert (Hockenhull, 83) Ghoddos (Trialist, 45), Carré (Adams, 15, Hercules, 90+1), Haygarth (Brook 72), Stevens, CramaSubs not used: Andersson, Koutsimouka