Valencia's bright start at the Emirates on Thursday was rewarded with Mouctar Diakhaby's away goal.
But Alexandre Lacazette quickly turned the game around with two goals in eight first-half minutes before Pierre-Emerick Aubameyang's late strike gave Arsenal a two-goal advantage to defend at the Mestalla on May 9.
However, Emery, who managed Valencia between 2008 and 2012, knows the tie is far from over due to Arsenal's terrible away record this season.
"It is a good result at home, but the second leg is going to be very difficult and maybe different. I consider for both teams it is 50-50," said Emery.
"We can be proud of the players. It is not easy to be calm and come back with that result against this team."
Arsenal are desperate not just for silverware in Emery's first season but the guarantee of Champions League qualification for next season that winning the Europa League would bring.
"We want to win the Europa League to go straight to the Champions League but also to win a trophy," said Lacazette.
"We want to finish in the top four in the Premier League and if we can go to Baku (for the Europa League final) it will be special."
A run of three straight Premier League defeats has left Emery's men needing more favours from Chelsea or Tottenham to stand any chance of Champions League qualification via a top-four Premier League finish.
The Gunners had conceded three times in all three of those defeats to Crystal Palace, Wolves and Leicester and the same defensive deficiencies cost them again early on.
Valencia had already missed a glorious chance to take the lead when Ezequiel Garay blazed over before Diakhaby forced the ball home at the back post for the vital away goal on 11 minutes.
Emery has been reticent to start Lacazette and Aubameyang together up front, but the game turned on one moment of magic from Arsenal's two prolific strikers.
Lacazette played in Aubameyang and the Gabon international left his marker and Valencia goalkeeper Neto on the ground before squaring for his strike partner to roll into an empty net.
Seven minutes later, Arsenal led as terrible defending allowed Lacazette a free header from Granit Xhaka's cross and a weak hand from Neto could not prevent the ball crossing the line.
"We had the game completely in control until their first goal," lamented Valencia coach Marcelino Garcia Toral.
"We played against two strikers that are very good which is why they cost the millions that they did. With the slightest error they punish you."
Lacazette missed two glorious opportunities to complete his hat-trick as he firstly failed to connect with an inch-perfect Aubameyang cross before Neto made a brilliant save at his near post to keep the Spanish side in the tie.
At the other end, Petr Cech also had to make a smart stop as he raced from his goal to deny substitute Kevin Gameiro.
The veteran stopper has announced he will retire at the end of the season.
And Cech's final game could well be against his former club Chelsea in next month's final as the Blues secured a 1-1 draw away at Eintracht Frankfurt in the first leg of the other semi-final.
Arsenal still have work to do, but they moved much closer to booking their trip to Baku when Aubameyang turned home at the back post in the final minute.
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