Unai Emery’s side will now face Chelsea or Eintracht Frankfurt in the final in Baku, Azerbaijan on May 25.
They were given an early scare when Kevin Gameiro opened the scoring for the hosts after just 11 minutes.
And the Gunners were perhaps lucky not to be 2-0 down by the time Pierre-Emerick Aubameyang cancelled out the away goal on 17 minutes.
Alexandre Lacazette made it 2-1 to the Gunners on the night five minutes after half-time and Gameiro made it 2-2 eight minutes later. But it was the outstanding Aubameyang who put the tie out of sight with 20 minutes left before sealing a superb night with two minutes left.
Here, Express Sport runs the rule over the players and their performances in Spain.
Petr Cech: Three shots faced and two conceded does not make for great reading. In truth, he could do little about both goals and a Europa League final will be a fitting swinging for a legend of the English game – 7 out of 10
Nacho Monreal: Not overly troubled as the third centre-back but Arsenal need an upgrade in the summer – 6
Laurent Koscielny: No huge errors but is no longer the commanding presence that Arsenal so desperately lack – 6
Sokratis Papastathopoulos: Exposed by the pace of Kevin Gameiro and should have tracked him for his second goal – 6
Ainsley Maitland-Niles: Youngster was targeted all night and often found himself out of position. Made up for it with a superb assist for Arsenal’s third goal of the night – 7
Sead Kolasinac: Pushed back for large parts and was not allowed to play his natural attacking game. poor overall. Subbed on 71 minutes for Shkodran Mustafi – 5
Granit Xhaka: The undoubted weak link in midfield and it is often difficult to see exactly what he offers. Failed to track runners and offered almost nothing going forward – 3
Lucas Torreira: Broke the play up well but was almost punished after giving away a free-kick within shouting distance. Luckily for him, Dani Parejo fired wide. Replaced by Matteo Guendouzi with 10 minutes left – 6
Mesut Ozil: A real calming presence when on the ball. Faultless in possession and eased the pressure when Arsenal were under the cosh. Replaced by Henrikh Mkhitaryan after an hour and – understandably – did not look happy about it. Booked – 8
Pierre-Emerick Aubameyang: Scored the crucial away goal early on and struck fear into Valencia at times with his pace and direct running. His second put the tie beyond doubt and he capped off a superb display with an emphatic third – 10
Alexandre Lacazette: Set up the equalising goal with a towering header and grabbed a superb one for himself in an all-action display. Top class both in and out of possession – 10
Henrikh Mkhitaryan: Did very little after coming on for Ozil. Days at the Emirates look numbered – 5
Shkodran Mustafi: Often the scapegoat but made few mistakes in his 20 minutes on the pitch – 6
Matteo Guendouzi: N/A
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