Josh Bohui's third goal in four matches proved to be only a consolation as Bolton Wanderers inflicted Brentford's first Under-18 Professional Development League Two South defeat of the season at a chilly Bolton Wanderers Academy this lunchtime.
The Bees dominated possession and territory for large periods of the match but were undone three times from set-pieces to suffer their first regular season defeat since January.
Alex Samizadeh put the hosts ahead just before the break with Danny McKenna making it 2-0 nine minutes into the second-half as he capitalised on some hesitant Brentford defending.
Alex Honeyball added a third shortly after and, despite Bohui pulling one back with 20 minutes to play, the hosts held on comfortably to record their second win of the season.
Jon De Souza's side showed five changes from last weekend's win over Cardiff City with Cameron Greaves, Romayne Pennant, Juan Pablo Gonzales Velasco, Terence Vancooten and Reece Cole all coming in.
Bolton, who dropped from a Category One to Category Two Academy over the summer, started the game slowly and it was The Bees who made all the running in the early stages without really threatening a goal.
The Bees were dominant in possession and territory but found it hard to break through into the final third while the hosts were reliant on the pace of Samizadeh to relieve pressure on their defence in the opening stages.
It took until the half-hour mark for either side to have a meaningful attempt on goal as Greaves and Chris Mepham dithered allowing McKenna to feed Samizadeh but his low shot was comfortably saved by Greaves.
If that was a warning shot for The Bees defence it was one that wasn't heeded as two minutes later more indecision in Brentford's backline was punished as Samizadeh nipped in to beat Greaves to the ball before steadying himself to roll home from close range.
Will Jaaskelainen, following in his father Jussi's footsteps, had been untroubled for most of the first period but when called upon he was off his line quickly to save at the feet of Ian Carlo Poveda.
Samizadeh could, and perhaps should, have doubled The Trotters lead before the break but he put his close range effort narrowly wide of Greaves' near post before, with the last action of the half, Max Allen fired a free-kick well over.
The opening stages of the second-half followed a similar pattern to the first with plenty of Brentford possession but very little end product.
The hosts were looking dangerous from set-pieces and it was from one such dead-ball situation that they doubled their advantage nine minutes after the restart, Kingsley Eshun was caught napping on the edge of the box as Brentford looked to clear a corner and McKenna finished clinically from 15 yards.
Samizadeh and Matthew Fearnley weren't seeing much of the ball but when it did come their way they were causing The Bees defence a host of problems with their direct running.
Fearnley teed up his strike partner who fired just wide before the game was wrapped up on the hour as McKenna's corner was thundered home by Honeyball, unmarked, at the back post.
Brentford tried to respond and Eshun was denied first by Jaaskelainen and then by Cole Lonsdale's goalline clearance after the home goalkeeper had fumbled an in-swinging corner.
The Bees did give themselves a lifeline with 20 minutes remaining as Lonsdale tripped Poveda in the box, Bohui calmly sending Jaaskelainen the wrong way from the spot.
Any hope was nearly extinguished a minute later as Samizadeh raced in behind but Greaves was off his line sharply to make a good sprawling save.
Vancooten did well to block another Samizadeh effort before two contentious referring decisions inside a minute denied Brentford a second-goal.
Francis Kale was perhaps lucky not to see red as he cynically ended Bohui's run to goal and from the resulting free-kick a tight call from the linesman denied Eshun his goal as he tapped home Luke Dunn's header.
As time ran down Brentford threw more men forward looking for a leveller and they were nearly punished as first Samizadeh's effort was blocked by George Harmes before Fearnley bravely charged down Greaves attempted clearance, the ball rolling inches wide of the post.
In the end three goals were enough for the hosts to pick up the three points and end Brentford's three game winning run ahead of next Saturday's home match with Huddersfield Town.
Bolton Wanderers: Will Jaaskelainen; Matthew Marsh, Francis Kale, Alex Honeyball, Cole Lonsdale; Ronaldo Pearson (sub Tyrell Palmer 76 mins), Luke Griffiths, Max Allen (sub Anas Abdo 68 mins), Danny McKenna; Matthew Fearnley (sub Jack Earling 90+2 mins), Alex Samizadeh Subs not used: James Aspinall, Jordan Grant
Brentford: Cameron Greaves; George Harmes, Chris Mepham, Terence Vancooten, Romayne Pennant (sub Luke Dunn 82 mins); Reece Cole, Giovanni McGregor; Josh Bohui, Ian Carlo Poveda, Juan Pablo Gonzales Velasco (sub Kingsley Eshun 46 mins); Courtney Austin (sub Anthony Guppy 68 mins)