Three second-half Wycombe goals three days previously had handed Scott his first defeat since taking the managerial reins temporarily following Terry Butcher's departure but this time it was three Brentford goals which gave Scott a second in four games and staked his claim well and truly for the full-time job.
Alan Connell got the ball rolling after just four minutes with a delightful chip over visiting keeper John Danby from Charlie Ide's slide-rule pass with the Chester back four appealing in vain for offside.
Glenn Poole almost followed up his Boxing Day belter with a second goal a few minutes later following a great passage of play between Connell and Ryan Dickson but pulled his shot wide.
And Ide should have done better on 21 minutes when put clear by a brilliant Gary Smith through-ball but Danby made a great save.
Connell then saw a goal disallowed for offside before Smith squared when he should have shot and the chance was gone as half-time approached.
The visitors offered little and Brentford continued to dominate after the break with Poole trying his luck from distance but coming up just short again.
Chester produced their only real effort on 65 minutes when sub Paul Rutherford tried a chip from the halfway line with home keeper Simon Brown off his line but the effort fell wide.
Brentford sub Ricky Shakes saw his shot deflected into the grateful hands of Danby soon after and Poole again fired over following a brilliant run from Shakes soon after.
But Brentford finally got the second goal their pressure deserved on 76 minutes when rookie striker Ross Montague headed his first goal in senior football from Shakes' cross.
And Poole finally came up trumps just three minutes later with a well-placed shot from the edge of the box past Danby's outstretched hand.