After sending Douglas Luiz off for a second bookable offence, Mike Dean then awarded the visitors a spot kick after Nelson Semedo brought down John McGinn in the box.
Anwar El Ghazi smashed the penalty home to give Villa all three points.
Joao Moutinho was also awarded a second yellow card just a minute later, meaning both teams finished the match with 10 men.
Goal Scoring Struggles
Wolves failed to score for a second consecutive game, following the 4-0 defeat to Liverpool.
However, that is not to say they have been without chances. In that time, Nuno Espirito Santo's men have accumulated 25 shots, 10 of which hit the target.
Since switching to a back four, Wolves have looked more dangerous going forward, creating numerous chances.
Wolves have been without their start striker, Raul Jimenez.
The Mexican is still recovering from a head injury suffered in the victory against Arsenal.
The creativity of these players really showed, and in the end, were unfortunate to come away empty handed.
If it wasn't for a Man of the Match display from Emiliano Martinez, Nuno's side could have easily walked away with three points.
It was Semedo's foul which gave the visitors a penalty in the 94th minute.
His error in the late stages of the match will no doubt grab headlines for the wrong reasons.
Statistically however, Semedo actually had a really promising game.
Surprisingly, Semedo finished the match with more touches than any other player on the pitch with 73.
The Portuguese full back also made the most clearances on the pitch with nine.
He also attempted five tackles which was only bettered by Moutinho who attempted nine.
Semedo completed four out of his five tackles, with the only failed tackle unfortunately ending in the match winning penalty for the opposition.
Going forward, the 27-year-old did his part and completed as many dribbles as Neto, who was also very impressive today.
Since his arrival in the summer transfer window, the former Barcelona man has raised questions over his defensive ability, however today's performance was arguably just two minutes away from being one of his best in a Wolves shirt.
Podence's Best Position
Podence returned to his role through the middle, where he played just behind the striker.
When he played there last, the Portuguese grabbed himself the winner at the Emirates.
Once again he looked really dangerous, particularly when he slotted through Silva after dribbling through the heart of the Aston Villa defence.
Podence finished the game with four shots, all troubling the gaolkeeper. This was more shots than any other Wolves player other than Silva.
In a 4-2-3-1 system which Nuno opted for today, Podence looks at his best in that central position, supporting the striker.
Long term, this could be the position which helps the 25-year-old reach his potential.