It completed a treble of victories over Unai Emery's side this season, following their home triumphs in the Premier League and Carabao Cup.
For Villa, it was a damaging defeat as they suffered back-to-back home defeats and perhaps more significantly, failed to get the win to put pressure on Manchester City ahead of their clash at Tottenham.
For Keith Andrews and his players, it was an incredible victory that saw them display remarkable defensive resilience as they became just the third team to win at Villa Park this season, joining Crystal Palace and Everton in doing so.
Brentford made three changes from the side that lost to Nottingham Forest last weekend, with Sepp van den Berg, Jordan Henderson and Dango Ouattara all coming in to the starting XI.
Brentford took the lead in first-half stoppage time through Dango Ouattara. (Image: PA)
Keith Andrews' side had their first opening chance came through Mathias Jensen, but he dragged his shot way wide of Emi Martínez's left-hand post.
After a quiet opening to the contest, the hosts thought they had finally broken the deadlock through Tammy Abraham, but Caoimhín Kelleher got down superbly to deny the striker.
Immediately in the aftermath, Kevin Schade could have given Brentford the lead, but he was unable to make firm contact following a knockdown in the penalty area.
Chances were suddenly coming like London buses, with Ian Maatsen lashing his volley well over the crossbar from Douglas Luiz's well-worked corner.
Dango Ouattara somehow failed to hit the target despite being one-on-one with Emi Martinez, though he was flagged offside but replays showed it was a tight call.
Like his defensive colleague Maatsen, former Brentford defender Ezri Konsa lashed over from a set-piece from which he should have done better.
Things took a twist when Brentford were reduced to 10-men just before the break.
A moment of madness saw Schade was sent off for kicking out at Matty Cash.
However, it would be the 10-man Brentford who stunned the vast majority of Villa Park in first-half stoppage time.
An teasing ball over the top found Ouattara, whose cross for Thiago was blocked, but the ball found its way back to the winger who smashed home past Martinez to give the visitors the lead.
Dango Ouattara celebrates with teammates after giving Brentford the lead at Villa Park. (Image: PA)
Unai Emery's side needed a quick response and they nearly had it through new signing Tammy Abraham.
Jadon Sancho's mazy run resulted in his shot being parried by Kelleher, with Abraham firing home the rebound.
However after a lengthy VAR check, it was adjudged that the ball had gone out of play at the other end and the striker was denied much to the fury of the home support.
Villa continued to probe and penetrate the Brentford goal but the visitors stood tall and were heroic to a man as they emerged worthy winners against a Villa side competing on several fronts this season.
Aston Villa: Martínez, Cash, Konsa, Torres, Maatsen; Luiz, Bogarde (Bailey ht); Sancho (Elliott 77), Rogers, Buendía; Abraham.
Brentford: Kelleher; Kayode, Ajer, van den Berg, Henry (Hickey 84); Janelt, Henderson (Collins 59), Jensen (Lewis-Potter 76); Ouattara (Yarmoliuk 60), Thiago, Schade.
Attendance: 41,415.