Nathan D'Laryea shepherded Moustapha Hadji's long ball back to Nicky Weaver but the City keeper made a hash of the clearance, allowing Luke Moore to score with a tap-in.
Joey Barton came closest for City in the second period, firing just wide from 35-yards, before Villa wrapped it up in injury time. Villa attacked after a City free-kick and Villa sub, Mika Aaritalo, scored past Weaver from the edge of the box.
That secured Villa's seventh straight win and keep them at the top of the table while Asa Hartford's side still have just a solitary victory so far.
City: Weaver, Warrender, Jordan, Wiekens, Bischoff (N D’Laryea 28), Neqouai, Flood, Barton, B Wright-Phillips, Bermingham (Murphy 79), Tandy
Subs: Ellegaard (GK), Collins, J D’Laryea.
Villa: Enckelman, Amoo, Jackman, Edwards (Cahill 59), Dublin, Davis, Hadji (Agnolahor 86), Hynes, S Moore, L Moore (Aaritalo 89), Bewers
Subs: Pecora (GK), Foley.
Attendance: 594