Striker Ryan Lowe was the hero, scoring two goals and having an assist in the third, as Chester ended their barren run which had stretched to eight games without a win.
Early on Kevin Ellison had tested visiting keeper Ben Hamer with a shot which was heading for the bottom corner until the stopper got down low to palm it away.
But it was Brentford who looked most likely to score, and they should have taken the lead on 24 minutes when Marcus Bean sidefooted an effort against the bar from inside the six-yard box.
The visitors were left to rue the missed opportunity when Chester went ahead a minute later, Eddie Johnson touching the ball into the path of Lowe, who raced through to finish confidently past Hamer.
Brentford had chances to level the game inside the first half, with Glenn Poole seeing a goalbound effort cleared off the line by Kevin Roberts and Bean forced John Danby into a save with a shot from the edge of the box, which the keeper pushed away low down to his right.
Chester then shocked their opponents by doubling the advantage on 57 minutes when a right-wing cross from Lowe was met by a bullet header from Kevin Roberts, which gave the visiting keeper no chance.
And on the hour mark, it was 3-0 as Lowe beat the offside trap to race on to Mark Hughes' pass and slide the ball in off the post. Chester could even afford to miss a great chance late on as Paul Rutherford was clean through on goal but hit the post.
The Bees rarely looked like finding a way back into the game although Moses Ademola headed a good chance wide ten minutes from time, as the visitors went down to their first league defeat since the opening day of the season.