Valencia also condemned the behaviour in a statement published on Friday and said it would take disciplinary action if those identified were season ticket holders, but claimed their fans may have been provoked by the Arsenal supporters prior to the incident.
Arsenal won the first-leg tie 3-1, with the reverse fixture in Spain on 9 May.
Arsenal playmaker Mesut Ozil has confirmed he wants to remain at the Emirates Stadium beyond this summer, according to Sky Sports.
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.
The Gunners came into the game in dismal form having suffered three successive Premier League defeats. Many of us are still drooling over Lionel Messi's magnificent performance for Barcelona in the Champions League but let's pause a second and gear up for another European night where two English Premier League teams face varying oppositions in the race to win the UEFA Europa League title.
Just like their north London counterparts Tottenham, the Gunners were startled by a fast start from their European visitors, culminating in a deserved opener from Mouctar Diakhaby, who rose higher than no less than three red and white defenders to nod his side in front with just 11 minutes played.
But Lacazette stopped Valencia in their tracks seven minutes after the hosts went behind.
Lacazette was denied a hat-trick on 66 minutes after Neto got down to block not one but two of his attempts.
Moments after Neto had made a superb save, Arsenal kept the ball alive and Sead Kolasinac's cross found Aubameyang at the far post to drive his volley home.