Villa's commanding lead was quickly erased after Amadou Onana lost possession to his former teammate Dwight McNeil, who skillfully placed the ball into Emiliano Martinez's net, leaving the home fans in disbelief.
Before long it was two. McNeil's right-wing free-kick was headed in from close range by Dominic Calvert-Lewin with Emiliano Martinez nowhere. A two-goal lead yet again for Everton and an opportunity to make amends for that extraordinary capitulation at home to Bournemouth last time out.
They blew it. Villa pulled one back before the break through Ollie Watkins and when Calvert-Lewin squandered an excellent one-on-one chance, Everton were punished. Watkins levelled when the stretching Jack Harrison only diverted the ball into his path.
Duran then settled it with an outrageous long-range strike soon after coming off the bench.
TrendingMartinez was left awe-struck at the other end and really would have been stunned had Calvert-Lewin not seen his shot hit the underside of the bar late on.
Jhon Duran was close to leaving Villa in the summer but he showed his worth once more with an astonishing strike to decide this game in their favour. Even more satisfying for Villa supporters, it came while Ollie Watkins was still on the pitch alongside him.
Much of the focus has been on whether Unai Emery can keep Duran happy, providing him with the minutes that he demands, and that is understandably awkward when Watkins is so important to his side. The England man showed that with his two goals.
But Duran is capable of dropping deeper, coming on as a replacement for Jacob Ramsey in this one. He will not always do so quite as spectacularly as this but his value to Villa is obvious. His eight Premier League goals have come at a rate of one every 86 minutes.
"I have seen it from behind and I saw the ball moving - it was unstoppable, it was a great strike," Martinez told afterwards. The Villa goalkeeper went on to discuss Duran's amazing potential, although his words of encouragement came with a caveat.
He added: "If he can keep the consistency he can be a really big threat. He can be one of the best strikers in the world, but he needs to keep his feet on the ground and to work hard. He has one of the top strikers in England playing in front of him."
"There's such a quick turnaround from the Euros. A lot of the boys are getting back up to fitness, and I am still not 100 per cent," Watkins told afterwards.
"I am disappointed I didn't get the hat-trick - I should be coming off with the match ball - but I'll settle for the two. I'm not at 100 per cent. I took some time off during the international break. I don't want to miss too many matches, though.
"We were obviously unlucky against Arsenal. We're delighted we got [the win] today. Now we focus on the Champions League, which everyone is looking forward to."
Aston Villa boss Unai Emery:
"I think his potential is a huge potential and I want to get the best from him, be supportive of him. And then he is getting confident. Even today he had chances to score two more goals.
"We are very demanding in our structure but we need the skills, the individual skill of the players, doing something special sometimes. Football is about being organised but it is also for the players. We are giving him confidence [to shoot], sometimes score, sometimes not."
Could Villa line up with Duran and Watkins together more in the future? "This is a process that I have in my mind to do. For me, it is not a problem, it is a solution."
Everton remain rooted to the bottom of the Premier League table having lost their first four games of the season for the first time in 66 years. That Sean Dyche's side have led half of those games by two goals will only add to the frustration felt by the club's fans.
This turnaround was more predictable than the late drama against Bournemouth but will be no more palatable for it. The third goal always felt needed and Calvert-Lewin had two clear-cut chances to provide it but his finishing in front of goal was wasteful.
"An absolute sorry state, the start Everton have made," said Jamie Carragher on co-commentary for . "It will have to change quickly."
Carragher added: "When I watch Everton, especially away from home, they play like a lower division team in the FA Cup.
"They weren't going to the Bernabeu here. they were going to Villa Park. Aston Villa are a good team but at one stage in the second half it was 75 per cent possession to Villa.
"Everton aren't brave enough to get on the ball and make passes.
"I said in the first half and at the start of the second half that there was no way Everton could just sit there and keep passing the ball back to Jordan Pickford and hang on."
Everton boss Sean Dyche told :
"We're certainly taking some knocks at the minute. Every mistake seems to be a goal, and every chance we don't quite capitalise on."
He continued: "Unfortunately we were on the wrong side of the margins again today. It's a tough one to take, for different reasons than the last game. We're down to a low squad anyway, so it's been a challenge - without a shadow of a doubt.
"We were terrific in the last game. It's one of those things. Today, we make a mistake and they capitalise on it. I said to the players, the killer instinct in both boxes is what's vital. The key moment was to go 3-1 up. We didn't and we made a mistake, and they capitalised on it. We have to keep going.
"We're making high-quality chances. At the minute, we've got to score as many as it takes to win a game. That's been a challenge since I've been at the club. We can't keep leaking goals like that."