Scott's revamped promotion-chasing side grabbed a vital win to leave Barnet pointless and hovering just above the trio of teams with negative equity in League Two.
Barnet almost took a first minute lead when livewire forward Adam Birchall made space in the area with a smart turn, but the former Arsenal trainee hooked his shot narrowly over.
It was Brentford who took the lead, however, when Brett Johnson's surging run was brought to an abrupt halt by Albert Adomah's clumsy challenge in the ninth minute.
Glenn Poole coolly sent home keeper Lee Harrison the wrong way and Brentford had the dream start they wanted.
But eight minutes later it was Poole who wasted a glorious chance to put the west Londoners 2-0 up when he miscued in front of goal after Charlie MacDonald had teed him up.
Barnet's threat was sporadically provided by Birchall and Adomah for the rest of the half, although Brentford striker Nathan Elder headed a decent chance inches wide after meeting an Adam Newton cross.
The restart brought immediate drama when, just one minute into the second period, Barnet were awarded a penalty.
This time around it was Johnson who returned the favour by tripping Adomah as he shaped to shoot on goal.
And, although it was Adomah who picked himself up and dusted himself down to take the spot-kick, his confidence somehow seemed to ooze away as he placed the ball.
His short run-up didn't fool Ben Hamer, who dived down to his left to palm the ball away.
Birchall was first to the rebound but could only drive into the side-netting, much to the dismay of the home crowd.
Just minutes later, Adomah thought he'd made amends when he unleashed a fierce drive from the edge of the area only for Hamer to brilliantly save his side once again.
On 68 minutes, Birchall almost grabbed a deserved equaliser but heartbreak ensued once more as his low drive beat Hamer but struck the post.
Craig Pead had a chance to seal the points late on but his weak volley was easily saved, before Birchall wastefully shot straight at Hamer from just four yards out with the easiest chance of the match.
Harrison tipped over from sub Moses Ademola late on as Barnet surged forward and got caught on the break.
But it was Brentford's day and they survived seven minutes of injury time to hang onto all three points.