Legia scored an early goal to take the lead in Poland from Pawel Wszolek, netting from close range before Jhon Duran equalised just three minutes later.
Summer signing Nicolo Zaniolo's blistering shot was rebounded into the path of the 19-year-old, who nodded in to score his first European goal.
But there was further surprise when Ernest Muci managed to give Legia the lead before a truly stunning strike from Lucas Digne gave Villa a much-needed equaliser before half-time.
Muci's strike needed VAR to confirm the goal after being close to offside but it came from poor defending as the Albanian lost Digne before tucking home.
However, the left-back made up for his error by smashing one into the top corner.
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John McGinn's shot led to panic in the box before it was cleared straight into Digne's path.
But there was plenty more to do as the ball set up for the half-volley, which the Frenchman greedily lapped up by lashing his effort with some pizzazz.
However, they went on to go behind yet again after Muci grabbed a second of the evening.
And once again, it was a defensive mishap for Unai Emery's men after the forward escaped his marker yet again.
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And that is how it ended as Emery appeared to underestimate his opponents as Villa tasted defeat on their return to Europe.
Villa have never played in the Europa Conference League, a competition that has only entered its third year of existence.
Even still, it has been some time since they have been in Europa at all.
They participated in the Europa League campaign of 2010/11, though that was not a long run at all.
Villa failed to even reach the group stage after being knocked out at the play-off round.
Rapid Vienna knocked them out over two legs, winning 4-3 on aggregate - which included a 3-2 win at Villa Park.
talkSPORT's very own Gabriel Agbonlahor was part of the squad that season at Villa and even scored in the tie.
However, he could not reverse Villa's fortunes in a season where Martin O'Neill lost his job and was replaced by Gerard Houllier.
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