Kevin Phillips gave the hosts a 12th minute lead at Walsall's Bescot Stadium but Blues were level just three minutes later through Mat Birley.
However, Villa regained the lead on 25 minutes through Paul Green.
Birley almost grabbed an equaliser for Blues on the hour mark but his effort was well saved by Villa keeper Stuart Taylor.
Villa secured the points 14 minutes from time when Craig Gardner made it 3-1.