The Gunners outclassed their hosts at the Estadio de Mestalla with a 7-3 aggregate win, to book a spot in the final billed for the Olympic Stadium in Baku on May 29.
After Kevin Gameiro broke the deadlock in the 11th minute, Aubameyang drew the visitors level on the night with his left-footed shot from outside the penalty area in the 17th minute.
Alexandre Lacazette fired the Gunners ahead in the 50th minute after benefitting from Lucas Torreira’s assist, but the lead was short-lived as Gameiro’s 58th-minute strike brought the hosts level again.
Aubameyang grabbed his second goal of the night in the 69th minute, and then completed his hat-trick after a one-two pass with Henrikh Mkhitaryan two minutes from time.
Thursday’s efforts stretched Aubameyang’s tally to 29 goals in 49 appearances across all competitions this season.