Agbonlahor, who put pen to paper on a four-year deal this week that ties him to the club until 2012, struck three times in just seven second-half minutes to grab the first treble of his career after Villa had threatened to throw away victory.
Villa dominated the game and deservedly took the lead through John Carew in the 47th minute.
But they briefly hit the self-destruct button allowing Elano to equalise from a 64th minute penalty.
Agbonlahor then came to Villa's rescue in stunning style to leave new City boss Mark Hughes with a major headache as even a last minute strike from Vedran Corluka couldn't hide their problems.
Troubled City must have sensed it would not be their day even before the game kicked-off.
Still reeling from last Thursday's shock UEFA Cup defeat at the hands of FC Midtjylland, City were stunned when they lost injury-jinxed striker Valeri Bojinov in the warm-up with an ankle problem.
They were extremely fortunate to get to half-time on level terms after Villa peppered their goal in the opening exchanges.
Carew set the tone after just six minutes when he headed an Ashley Young cross wide, before Young saw his shot blocked by Michael Johnson.
Carew was a constant menace to City and twice in the space of two minutes it needed smart saves from Joe Hart to deny the Norway international.
City, who threatened briefly through Kelvin Etuhu when he shot just wide after turning away from Nicky Shorey, had another double let off when Gareth Barry's finishing let him down.
He fired just wide in the 26th minute when Hart tipped a cross from Nigel Reo-Coker into his path and was then denied by his England team-mate.
Some last ditch defending by Micah Richards, who cut out Barry's centre as Agbonlahor prepared to pounce, rescued City on the stroke of half-time, before Reo-Coker was inches away from meeting a cross from Young.
City's charmed life could not last for ever and Villa's pressure finally told just two minutes after the interval.
Young made another trademark run down the wing and fed Carew, who made no mistake with a far post header.
Ironically that sparked City into their best spell of the match. Brad Friedel had to tip Javier Garrido's low angled drive around the post, before Martin Petrov fired into the side-netting when well placed.
Villa still looked untroubled and it was no surprise that it took a mistake from Martin O'Neill's side to let City back into the game from the penalty spot.
Johnson's surge into the area was ended by a foul from Luke Young and Elano converted from the spot.
But all that did was set the scene for Agbonlahor to steal the show.
The England Under-21 international opened his account with a spectacular close-range volley in the 69th minute after Curtis Davies had nodded an Young corner back across the face of goal.
He then ended City's challenge five minutes later with a neat far post header following a left wing centre from Barry.
Barry also set up his third in the 76th minute after releasing Agbonlahor, who raced clear before curling his shot around the helpless Hart.
City did at least manage to end the match on a high when Johnson fed Corluka and he beat Friedel from close range but it was scant consolation.