The young Bees fell behind to an early Amadou Traore finish before the hosts kicked on in the second period to net through Gabriel Lemoine and Loic Bessile.
Arthur Read would ensure that the young Bees would get on the scoresheet in the dying seconds of the game as he slotted home following good hold-up play from Gustav Mogensen.
The home side started the brighter with an intense press putting the Brentford back four under significant pressure early on. And that intensity showed when they forced Aubrel Koutsimouka into a misplaced pass before Traore picked it up and slotted low into the corner past Nathan Shepperd.
After riding out the early pressure Brentford B began to assert themselves on the game a bit more and had a good chance when Matej Majka pulled the ball back from Jaakko Oksanen to shoot but for a good defensive block.
Christian Tue Jensen would then attempt to replicate one of his excellent free-kick finishes that have served him well so far this season, but the Dane was just off target despite making the Bordeaux keeper scramble to his right-hand post.
A Brendan Lebas volley would follow just after the half hour mark as the French side reminded the Bees of their counter-attacking threat.
A big chance then fell for Koutsimouka just before the break when a whipping corner from Tue Jensen found the defender unmarked, but he was unable to keep his header on target as it edged just over the crossbar.
Tue Jensen would see his second free-kick saved early in the second period which preceded the second goal of the game, and unfortunately for The Bees, it went against them. After Nick Tsaroulla was dispossessed out wide on the left, Lemoine was set free and managed to hold off Kane O’Connor before cutting onto his left foot and finishing clinically.
It would get worse just after the hour mark when the French side added a third from a set piece. A whipped in free-kick from the left found Bessile who thumped a header into the back of the net to put the hosts firmly in control.
Few chances would fall in the later stages of the game bar a David Titov cross which was claimed well and a Mogensen header which edged the wrong side of the post.
But in the 92nd minute the young Bees managed to get themselves on the scoresheet as a ball was stood up to the far post which saw Mogensen rise well to nod into the path of Read who finished well.
The Bees will set their sights on a trip to Portugal on Saturday where they will take on FC Seoul and FC Astana.
Brentford B: Shepperd, Tsaroulla, Yearwood, Koutsimouka (Mitchell, 67), O’Connor, Adams, Zamburek, Majka (Mogensen, 57), Tue Jensen (Carre, 57), Titov, Oksanen (Read, 57)
Subs not used: Trialist
Bordeaux XI: Malbec, Lacoux, Carrique, Bessile, Dedioub, Boujouaha, Delaurier, Depussay, Traore, Zerkane, Lebas
Subs: Cardoso, Compper, Orea, Lottin, Semedo, Haruna, Lemoine, Mamoudi