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Former Arsenal boss Emery holds a 2-1 lead over his old club in the semi-final tie going into Friday's (AEST) second leg.
Manu Trigueros and Raul Albiol had given Villarreal a two-goal lead in the first leg and the Gunners looked doomed when Dani Ceballos was sent off.
But a controversial penalty that was won by Bukayo Saka and scored by Nicolas Pepe ensures that it is all to play for in the return fixture.
Villarreal have progressed from 15 of their 16 two-legged ties in major European competition when winning the first leg.
But the only exception was against an English club at the same stage of the same competition - in a tie against Liverpool in 2016 - and Emery feels Arsenal are the most likely team to progress.
"The first-leg result doesn’t change my initial thoughts on the competition," Emery said at his pre-match news conference.
"Arsenal started as a favourite and they are still favourites at this stage. The first-leg result is too narrow to make a big difference.
"We have to try to compete with these types of teams.
"When I analyse our opponents, the first thing I do is study them and try to prepare to play against them at their best.
"Arsenal are structurally solid, they can keep possession, combine well, and have quick and technically-gifted players.
"We are going to see Pierre-Emerick Aubameyang, so we will face the best Arsenal side, both collectively and individually."
Gerard Moreno has either scored or assisted in each of his seven starts in the Europa League this season (six goals and three assists).
Arsenal, who are relying on the Europa League to salvage their campaign, know a place in next season's Champions League is the reward if they win the competition.
They have progressed from each of their last two European knockout ties where they lost the first leg.
And not since 1995-96 have Arsenal failed to qualify for European competition of some sort, with Mikel Arteta acknowledging the importance of keeping that run going in his own pre-match news conference.
While he thinks his side are underdogs, Emery is keen to highlight the significance of this accomplishment.
"It is a very beautiful moment for us," he said.
"We have been working throughout the year trying to build on our confidence, results and objectives, and in the Europa League we’ve had a fairly solid campaign so far.
"We are approaching the game in the same way we did the first leg.
"We will build on our performance in the previous 90 minutes. We are 2-1 up, but that doesn’t change anything. We are going to try to be ready for whatever lies ahead."
Arsenal has lost just one of its 11 knockout games with Spanish opponents at home, with that loss coming against Barcelona in the Champions League last 16 in February 2016.