Wolves made the breakthrough in the 25th minute of the clash, with Matheus Cunha firing one into the bottom corner off the post after collecting a loose pass from Diego Carlos.
Rayan Ait-Nouri almost had a second for the visitors shortly after, with his deflected effort whistling just wide, but Villa managed to end the first half on top despite having nothing to show for their efforts in the opening 45 minutes of action at Villa Park.
Wolves were the dominant outfit in the first period, having 10 shots to Villa's two, but the visitors did require a poor piece of defensive work from Carlos in order to make the breakthrough.
An apparent hamstring injury for John McGinn made it an even more difficult first half for Villa, and it was Wolves that were looking the most likely in the second period, with Cunha the obvious threat.
However, the leveller came in the 73rd minute of the match, with Ollie Watkins collecting a pass from Morgan Rogers before forcing the ball home to break the Wolves resistance.
Emery's side then scored a second in the 88th minute of the contest through Ezri Konsa, with the defender firing home at the far post to break Wolves hearts at Villa Park, before Jhon Duran scored a third for the hosts in the final exchanges to make sure of all three points.
Villa have risen into third spot in the Premier League table, boasting 12 points from their first five matches, while Wolves have dropped to 20th, with Gary O'Neil's side only collecting one point from their first five games.
VILLA VS. WOLVES HIGHLIGHTS
25th min: Aston Villa 0-1 Wolves (Matheus Cunha)
Wolves make the breakthrough at Villa Park, with Cunha sweeping one into the bottom corner off the post after some poor defensive work from the home side.
Carlos gave the ball away in a dangerous area, and Cunha advanced into a shooting position before finding the back of the net with an excellent strike.
73rd min: Aston Villa 1-1 Wolves (Ollie Watkins)
Villa level the scores in the 73rd minute of the contest, and it had to be him.
Watkins collects a clever pass from Rogers before beating the onrushing Sam Johnstone.
88th min: Aston Villa 2-1 Wolves (Ezri Konsa)
Villa score a second to break Wolves hearts in the latter stages, with Konsa turning home at the far post; Wolves were heading for a huge point, but they have conceded a late second.
93rd min: Aston Villa 3-1 Wolves (Jhon Duran)
Villa well and truly make sure of all three points in front of their own supporters, as Duran, who has made a strong start to the season, pokes a cross from Rogers into the back of the net.
It was tight in terms of offside, but the goal is eventually cleared.
MAN OF THE MATCH - MATHEUS CUNHA
Wolves will do well to keep Cunha on a long-term basis, as the Brazilian is a brilliant player; his pace and power caused Villa problems throughout the contest, and his goal was a brilliant strike.
The 25-year-old had two successful dribbles at Villa Park, while he also finished with a pass success rate of 88%, with Cunha using the ball intelligently throughout his 90 minutes on the field.
Rogers deserves a mention for his two late assists for Villa, but even though Wolves lost, Cunha was the best player on the pitch and could not be denied for the man-of-the-match award.
VILLA VS. WOLVES MATCH STATS
Possession: Villa 52%-58% Wolves
Shots: Villa 9-10 Wolves
Shots on target: Villa 4-4 Wolves
Corners: Villa 6-5 Wolves
Fouls: Villa 11-6 Wolves
WHAT NEXT?
Villa will now switch their attention to the EFL Cup, preparing to tackle Wycombe Wanderers in the third round of the competition on Tuesday night, before heading to Ipswich Town in the league next weekend.
Wolves, meanwhile, lost in the third round of the EFL Cup last week, so they do not have a mid-week fixture, instead returning to league action at home to Liverpool next weekend.