The England international hit two against the Barclays Premier League champions, semi-finalists in this competition in two of the last three seasons.
Mario Balotelli and then Aleksandar Kolarov had twice put the hosts ahead while Villa old boy Gareth Barry's helped his former team's cause with an own-goal equaliser and Agbonlahor took the tie to extra-time.
Charles N'Zogbia scored only his third goal since his summer 2011 move from Wigan to put Villa ahead early in the added period, and Agbonlahor ensured there was no way back with his second goal seven minutes from the end.
Meanwhile, two moments of individual magic was enough for 10-man Sunderland to see off a spirited MK Dons side 2-0 at Stadium:mk.
The game lacked quality for large periods but two second half goals, a fantastic Craig Gardner free-kick and a well-taken solo effort from James McClean, secured a safe passage into round four for Sunderland.
Martin O'Neill saw his captain Lee Cattermole sent off for the fifth time in his Sunderland career for a nasty first-half challenge on MK Dons defender Adam Chicksen but the Barclays Premier League outfit still had just enough in reserve to see off their npower League One hosts.
Source: PA
Source: PA