An injury time penalty denied Rovers a point after a rollercoaster match ended in the cruellest possible way for the hosts.
Cole Stockton’s late equaliser looked to have earned a share of the points, after strikes from Chris Atkinson and Adam Dugdale had hauled Rovers back from 2-0 down.
However, Dugdale was adjudged to have handled in the box after the clock has passed 90, and Adam Forshaw’s spot kick meant the points were Brentford’s.
Ronnie Moore made one change to the side that drew with Stevenage last week, with Owain Fon Williams replacing Jason Mooney in goal, following his return from international duty.
Fon Williams was involved early on as Rovers made the worst possible start, after three minutes the goalkeeper could only parry Harlee Dean’s effort, allowing Martin Taylor to prod home the opener on his Brentford debut.
The visitors had their tails up in the opening stages and Clayton Donaldson then cut in on the right and shot wide, before Will Grigg shot at Fon Williams soon after.
Former-Rover, Shay Logan, was next to threaten, firing narrowly over with a left footed drive.
The one way traffic continued, and on 14 minutes Brentford doubled their lead. Moments after Donaldson set up Toumani Diagouraga to hit the upright, the big striker slammed home the second from close range.
Rovers then began to ease themselves into the game, and Danny Holmes forced Richard Lee to tip behind for a corner.
Ian Goodison then won a corner after a speculative shot, but Rowe fired well over the bar from the resulting set piece.
Will Grigg’s cross-cum-shot was then kept out by Fon Williams at full stretch. Whilst for Rovers, Goodison’s header was held comfortably by Lee.
The game was back alive a minutes before half-time when Atkinson halved the deficit, the midfielder benefited from a number of ricochets inside the Brentford box, before slotting home.
After the break Rovers looked to draw level, and James Rowe’s drive was spectacularly kept out by Lee.
From the next attack the hosts deservedly levelled. Rowe’s cross was right on the head of Joe Thompson, and although Lee kept out his header, Dugdale rammed home the rebound to equalise.
The game was now well and truly in the balance, and Brentford were the next to threaten, with Dean heading wide.
Disaster struck soon after however, when Logan’s cross was met by Donaldson, who’d outmuscled Dugdale, before heading past Fon Williams.
Dean looked to put the game out of sight for the visitors, but his drive was deflected off target.
The action was relentless, and moments after Atkinson’s goal bound effort was blocked, Brentford counter attacked rapidly, with Donaldson firing wide.
With around ten minutes remaining Moore twisted, with Andy Robinson and Stockton replacing Thompson and Ryan Lowe.
Donaldson remained the main thorn in Tranmere’s side, with the big striker turning and firing just over.
With a minute left on the clock Abdulai Baggie, fresh from international duty, replaced Rowe.
And with that minute remaining, Rovers used it to equalise, with Moore’s substitutions doing the trick.
Baggie, instantly involved, set up Max Power, whose teasing cross was steered past Lee by Stockton.
However, as the game entered injury time there was one last cruel twist for the hosts.
Dugdale, the second goal scorer, was penalised for hand ball in the penalty area, and Forshaw smashed the penalty into the roof of the net to claim the points for Brentford.
Tranmere: Fon Williams, Holmes, Dugdale, Goodison, Horwood, Thompson (Robinson 78), Power, Atkinson, Rowe (Baggie 90), Lowe (Stockton 78), Akpa Akpro. Unused substitutes: Mooney, Jones, Taylor, Sodje.
Brentford: Lee, Forshaw, Craig, Dean, Donaldson, Grigg (Trotta 87), McCormack (Fillo 60), Logan, Saville (Teixeira 90+2), Diagouraga, Taylor. Unused substitutes: O'Connor, El Alagui, O'Brien, Reeves.
Referee: Scott Duncan
Yellow cards: Akpa Akpro (80), Robinson (83)