Tempers flared as players from both sides clashed on the final whistle, but it was Unai Emery's side left celebrating as they booked their place in Baku, where they will face Chelsea or Eintracht Frankfurt on May 29.
After Liverpool and Tottenham reached the Champions League final in the most dramatic of circumstances this week, Arsenal put in a commanding performance at Valencia to ensure their lead would not slip.
Aubameyang, who signed for Arsenal from Borussia Dortmund in January a year ago, was ineligible for the Europa League last season when the Gunners fell at the semi-finals to eventual champions Atletico Madrid, failing to take advantage of a red card in the first leg and losing 2-1 on aggregate.
Chelsea and Arsenal enjoyed plain sailing through their respective Europa League groups with both teams collecting 16 points from a possible 18, albeit against unfancied rivals.
A hat-trick from Pierre-Emerick Aubameyang and an Alexandre Lacazette strike booked Arsenal's place in the Europa League final with a 4-2 win at Valencia to seal an emphatic 7-3 aggregate victory.
Arsenal goalkeeper Petr Cech is relishing playing his former club Chelsea in the Europa League final, which could make for a "remarkable end" to his glittering career.
It's unlikely that Mkhitaryan would start against Chelsea anyway after Aubameyang, Lacazette and Mesut Ozil played so well against Valencia, but having him on the bench as another option is vital.
"Last night's game demonstrates that anything can happen", he said at his pre-match press conference.
"Unfortunately, we have to go to the U.S. to play a match".
Tottenham Hotspur beat Ajax 2-3 in the second leg of the Champions League semi-final thus securing a berth in the final which is scheduled to be held in Madrid.
"I think Emery, even if he loses the final, has seen a good improvement in Arsenal". Today was really good and we played against a very hard team and we are very happy. "It's all so handsome, so attractive, that it does not allow us to go further", Marcelino added.
Valencia looked like they could score six let alone the one more required, only for Arsenal to find an equaliser against the run of play.
"The last dream was to play this European final and it has come true".