But Agbonlahor continued his hot scoring streak after linking up with fellow striker John Carew to seal a spot in the fourth round.
The England striker was on target for the fourth successive match - with a cheeky back-heeled finish on three minutes - to kill off the challenge of the gallant Bluebirds and seal a sixth straight win for Villa in all competitions.
But the future looks bleak for Villa midfielder Nigel Reo-Coker after he was not even named among the substitutes following his much-publicised training ground spat with Villa boss Martin O'Neill last week.
O'Neill made five changes but still retained a core of experienced players and skipper Stiliyan Petrov, winger James Milner - despite a missed penalty - and defenders Carlos Cuellar and Nicky Shorey all had fine games.
But Cardiff, whose boss Dave Jones made six alterations to his line-up, were far from overawed and had opportunities to at least take the game into extra-time in a much-improved showing after the weekend home defeat by QPR. Midfielder Peter Whittingham in particular impressed on his return to Villa Park.
Villa Park was barely half-full despite the presence of 3,000-plus Cardiff fans but after three minutes the home side went ahead through Agbonlahor.
Carew was the creator with a run down the right flank before sending over a low cross.
Agbonlahor was first to react at the near post and his deft flick flew past his former Villa team-mate Peter Enckelman into the far corner of the net.
Gabor Gyepes had a golden chance to equalise when he got on the end of an inswinging free-kick from Whittingham but from six yards out he headed over the crossbar.
Milner was not afraid to shoot with one effort cannoning off Adam Matthews for a corner and another producing a low save from Enckelman.
But Cardiff were creating chances and Brad Guzan, deputising for the rested Brad Friedel, did well to keep out a deflected drive from Gavin Rae.
Bluebirds skipper Joe Ledley then headed over after a cross from Chris Burke had posed problems for the home side.
Milner showed his trickery in twice turning past Matthews and his eventual cross-cum-shot curled just past the far post with Enckelman scrambling along his line.
Carew sent a glancing header wide from a Milner corner but Cuellar had to be alert at the other end to block a shot from Jay Bothroyd in a quick Cardiff counter-attack.
Enckelman got his body behind a low drive from Villa skipper Petrov just before the interval.
Carew had a good opportunity to double Villa's lead after two minutes of the second half. A crossfield ball from Fabian Delph found Milner in space and his cross picked out Carew at the far post but the Norway international headed wide when he should have at least hit the target.
The visitors had a let-off after 58 minutes when Milner missed from the penalty spot. Petrov was brought down in the area by Gyepes who was also yellow-carded for the foul. Up stepped Milner but he crashed his shot against the woodwork.
Jones brought on top scorer Michael Chopra in place of Riccardo Scimeca after an hour and Delph then became the first Villa player to be cautioned for a challenge on Whittingham.
Guzan was the equal of a curling 30 yard free-kick from Whittingham and Habib Beye was yellow-carded for a foul on the same player as Cardiff pressed for an equaliser.
Bothroyd had the ball in the net in injury-time but the flag was already raised for offside.