Villa struck in just the ninth minute as Philippe Senderos got in front of Dejan Lovren to meet Ashley Westwood’s corner, with Agbonlahor pouncing in the six-yard box to poke the ball home.
From that point on, Paul Lambert’s men defended in superb fashion with Senderos and Nathan Baker excellent as they repelled everything Liverpool had to throw at them.
Brendan Rodgers’ side never really tested Brad Guzan in a limp attacking display, with the closest they came to levelling coming when Philippe Coutinho hit the post and substitute Raheem Sterling fired the follow-up against Jordan Henderson.
Villa are now up to second in the table after an excellent start to the season, but Rodgers has much to ponder ahead of their UEFA Champions League return.
With Daniel Sturridge sidelined for up to three weeks with a thigh injury – for which Rodgers has still not forgiven England – it meant Liverpool started a game without him or Luis Suarez, a summer departure to Barcelona, for the first time since December 2012.
Last season the pair scored 56 league goals between them so it was immediately apparent where the Reds were most likely to be under the greatest strain.
Lambert knew this, and also the fact their opponents have still not entirely cracked defending set-pieces, and that was what he targeted.
Liverpool were denied space in the final third which stifled much of their forward progress, while the visitors attacked with speed when they had the chance and were aggressive at corners and free-kicks – which ultimately produced their winner.
Mario Balotelli was brought in by Rodgers last month to provide additional firepower but he spent much of the first half either being kicked or trying to avoid being kicked by Senderos.
The Swiss defender got away with at least one blatant hack at the former Manchester City striker off the ball which would have likely resulted in a card had referee Lee Mason or either of his linesmen seen it.
Whether it knocked Balotelli, making his home debut, off his stride or not it was the latter stages of the half before he started to show signs of life with one viciously-dipping shot with the aid of a deflection off Andreas Weimann dropping just wide of the post.
He also created a good chance for Adam Lallana, making his debut after injury in pre-season delayed his first appearance since a summer move, but the former Southampton midfielder drilled a half-volley just wide from Balotelli’s lay-off on the edge of the area.
By that time Liverpool were already behind after mistakes by their two centre-backs.
First Mamadou Sakho tried to control the ball close to his own goalline instead of playing safe and ended up conceding a corner, from which Lovren got the wrong side of Senderos whose header created a scramble from which Agbonlahor scored in the ninth minute.
The goal was against the run of play as Lazar Markovic, also making his first Anfield appearance, had already volleyed over Alberto Moreno’s far-post cross and headed wide after being involved in good build-up play with Henderson and Javier Manquillo.
While Lallana was deservedly booked for a late challenge on Tom Cleverley, making his debut after a deadline day loan move from Manchester United, Mason missed Senderos’ kick at Balotelli and chose to take no action after Alan Hutton appeared to rake his studs down the Italian’s knee.
Senderos could have rubbed further salt into the wound but headed a free-kick over when well placed and then blasted wide from close range at another corner.
Balotelli had the first chance of the second half, heading wide Steven Gerrard’s corner.
Sterling’s introduction, having been rested after international duty, on the hour raised the temperature a notch or two with Hutton booked for scything down the youngster within seconds of his arrival.
Villa’s plan to smother Liverpool continued to work, however, and even the introduction of Rickie Lambert and Fabio Borini for Balotelli and Markovic failed to produce the chances needed to rescue a point.
The closest they came was when Coutinho bent a shot around goalkeeper Guzan only for it to rebound back off the post as Villa left Anfield having taken their tally to eight points from their last four visits.