City defender Robert Huth got a last ditch winner on an emotional day for the Potters, and more so Tony Pulis.
City manager Pulis missed the first half of this game after his mother passed away earlier in the day but reappeared for the second period and helped City turn a 1-0 loss into a 2-1 victory.
City dominated the opening exchanges and Jones was at the forefront of the Potters attacks as he headed over after crosses from Delap and Etherington, saw a shot saved by Freidel after a sublime through ball from Wilson and also saw a ferocious 30 yard shot well held by the keeper.
All this was undone when the visitors broke the deadlock on 34 minutes as Agbonlahors raking cross was converted via a diving header from Downing.
Although City should have a penalty soon after courtesy of a James Collins handball, they were actually thankful to be just the one goal behind at the break after Young missed from 2 yards and Downing had a second shot saved by Sorensen.
The crowd gave manager Tony Pulis a standing ovation at the start of the second half as he appeared from the tunnel but even with the gaffers presence Villa's defence seemed to cope better after the break and although City had much more possession the chances were few and far between as Villa sat deep inside their own half.
The defence was undone though twice late on as Etherington crossed for Jones to power in a header in the 79th minute before Huth stabbed in from close range after Etherington sent in a low cross in the 94th minute.