Agbonlahor's second goal of the season was Villa's one real goal opportunity of the game which summed up a tense battle.
Birmingham could certainly feel hard done by at the end of a match in which they had more of the attacking play than Villa.
It was certainly a much-improved local derby performance from Birmingham but they could not prevent themselves slipping to their fifth successive defeat against their old rivals.
Birmingham demonstrated their recent good form with a positive performance as they were always prepared to attack.
As a result Villa, who included three new signings, Richard Dunne, Stephen Warnock and James Collins, were unable to build up many attacking moves.
The raw tenacious approach of Birmingham put Villa out of their stride and it was significant that Ashley Young, without the service usually provided by Nicky Shorey, was unable to operate as freely as usual.
James Milner had Villa's best chances in the first half from openings created by Agbonlahor but on each occasion the England man was off-target.
Birmingham were similarly restricted. Garry O'Connor managed to fire off a vicious left-foot shot only to see his effort deflected in turn by Dunne and Warnock.
A great deal of credit for Birmingham's battling performance can be attributed to the likes of Barry Ferguson who has really settled to life in the Premier League following his arrival from Rangers.
Franck Queudrue and Roger Johnson also played a major role in the heart of Birmingham's defence which was the reason for Villa's limited goal opportunities.
James McFadden was unable to resume for the second half because of a leg injury and was replaced by club skipper, Lee Carsley - the only Birmingham-born player in the home side.
A helter-skelter type of game continued after the break, and when the industrious Seb Larsson did break he was pulled back by Steve Sidwell who was booked by Howard Webb for his transgression.
Larsson, making his 100th league appearance for Birmingham, could not be faulted for effort and his strong running did much to keep the Blues in the match.
It was not until the final 15 minutes that Villa suddenly applied pressure and Joe Hart distinguished himself with a close-range save to keep out a header from Sidwell.
The only goal occurred after Stuart Parnaby had been booked. Young's free-kick was headed on by substitute John Carew to the unmarked Agbonlahor who guided the ball past Hart.