Referee Gavin Ward point to the spot deep into injury time and the Bees No.7 converted.
North End boss Simon Grayson had been forced into making two changes with Bailey Wright (ankle) and Will Hayhurst (hamstring) both ruled out, Chris Robertson and Jack King both coming in and their injury problems continued in a goalless first half, losing both John Welsh and Lee Holmes, John Mousinho – against the side that gave him his professional debut – and Keith Keane their replacements.
It was a high tempo first half, with the big, physical home side testing North End’s defensive capabilities and the Lilywhites relying on breaks.
The first PNE chance came after only five minutes, Stuart Beavon finding himself in a left hand channel; he slotted the ball back to Jack King and it came off a defender, but King couldn’t convert with Simon Moore claiming.
Ten minutes in there was a great back-tracking save by Declan Rudd after Donaldson’s 25 yard effort deflected up and looped goalwards.
And three minutes later Rudd was in fine form again to deny Donaldson after a swift break from the midfield.
With 20 minutes left in the half, a Good break from PNE, King and Beavon running at the Bees defence, out to the right and Holmes fires just wide of the right hand post.
The home side’s best chance of the half came eight minutes before the break, as David Buchanan headed off line from Harlee Dean after great flicked header from a Brentford left wing corner.
A few seconds later, a great chance fell for for North End. Beavon deep in left hand channel pulled the ball back for the onrushing Jack King, but his side-footed effort was just wide of the right hand post.
The second half saw North End again having to defend resolutely and were happy to see Jonathan Douglas fire over ten minutes into the half when Declan Rudd appeared to be fouled.
With 16 minutes left Bees substitute Jake Bidwell lined up a free kick 25 yards out just right of the 'D', but Sam Saunders took it and it took a brilliant save from Declan Rudd to tip the ball over for a corner.
In the final ten minutes Stuart Beavon burst onto a Keane bal and drove inwards, unleashing an effort from 25 yards, but it was wide off the right hand post.
In the final minute another free kick for the home side was given on the edge of the box Saunders again teed it up, but this time it was over the bar as the game entered the four minutes of stoppage time.
But in the third minute of stoppage time a penalty was awarded to the home side - for what no one was sure - but it gave Saunders the chance to win the game; and he did firing high into the top right hand corner giving Rudd no chance.
PNE line-up: Rudd, Connolly, Buchanan, Welsh (Mousinho, 34), Huntington, Robertson, Holmes (Keane, 46), Wroe, Beavon, King (Cummins, 88), Garner. Subs not used: Stuckmann, Monakana, Procter, Foster.
Brentford line-up: S Moore, Craig (Bidwell, 55), Dean, Saunders, Donaldson, Adeyemi (Forshaw, 65), Logan, Wright-Phillips (Trotta, 71), Diagouraga, L Moore. Subs not used: Dallas, Gounet, Forrester, Reeves.
Referee: Mr Gavin Ward