Foxes fans were aggrieved at the result because for long periods Leicester were the better team, making a mockery of the supposedly gulf between the sides.
As it was, Martin O'Neill's men needed the help of a controversial penalty and a goal in the last minute of extra-time to finally subdue their resolute opponents.
City - robbed by injury of six first-team regulars - started brightly enough but it was Villa who took the lead in the sixth minute with their first attack of the game.
Agbonlahor made inroads down the right before crossing the ball low into the danger area where it was tucked home from six yards by Juan Pablo Angel.
City worked hard to get back into the game but it was Villa who threatened again on 17 minutes when Paul Henderson needed two attempts to kill a long-range effort from Stilian Petrov.
Leicester continued to press with Gareth Barry having to head Momo Sylla's dangerous free-kick out for a corner and Elvis Hammond's 22-yard drive forcing Stuart Taylor into a sprawling save.
But it was Villa who went close to doubling their advantage on the half-hour mark when a corner by Milan Baros was flicked on by Agbonlahor for Angel to head against the bar.
But five minutes before the break Leicester were level when Sylla's free-kick was only half cleared to Iain Hume whose ten-yard shot was beaten away by Taylor and Richard Stearman was first to react to hammer the ball home for his third of the season.
Villa regained the lead in first-half time added on when Gareth McAuley was harshly ruled to have impeded Petrov inside the box. Barry blasted the resultant penalty into Henderson's top left corner.
Leicester began the second half in determined mood with Hume ending a mazy run with an edge of the box shot which fizzed just beyond an upright.
Leicester continued to enjoy good possession but without creating much of a threat on the Villa goal.
However, all that changed on 84 minutes when Patrick Kisnorbo met a Sylla corner at the near post to score with a downward header.
Then deep in time added on there was heated controversy when Sylla was ruled to have pulled the shirt of substitute Chris Sutton inside the box.
Sylla was shown a yellow for the foul and Kisnorbo similar for protesting. The referee's retribution hadn't finished there with City's assistant manager Mike Stowell banished to the stands.
When the storm subsided Henderson showed he had kept a clear head, diving to his left to push away Barry's spot-kick and send the tie into extra-time.
In the first period of extra-time Henderson denied Petrov and then in the second period the keeper shone again when he twisted in mid air to keep out a thunderbolt from Barry.
But in the final minute tragedy struck when City failed to clear their lines and Agbonlahor took full advantage to drive home an angled shot from ten yards which appeared to take a deflection off McAuley.