With four minutes remaining at the Calderon on Thursday, Valencia substitute Nikola Zigic was left with a torn shirt after being pulled back by Atletico defender Juanito as he went for a header at goal.
The Serbian striker's team-mates surrounded German referee Florian Meyer to protest but were waved away, and their coach Unai Emery was sent to the stands to watch the rest of the 0-0 draw, which saw Valencia go out on away goals.
"You have all seen it, the television doesn't lie. When you decide to have extra officials it is so this type of incident doesn't happen," Emery was quoted as saying in Spanish media on Friday.
UEFA is experimenting with five-man teams of officials in this season's Europa League matches, two additional assistants being positioned beside each goal to help the referee judge incidents inside the area.
"We believe the referee didn't have the strength of character (to give the decision), neither did his assistants," Emery added. "When they see the incident they will be ashamed."
Valencia goalkeeper Cesar unsurprisingly backed his coach.
"I can't believe they didn't see it," he was quoted as saying.
"To blow for a penalty in the 86th minute for the visiting team in the return leg of a knockout competition, you need to have great strength of character.
"Next year, I won't bring my watch in case they steal that as well."
Atletico, who went through courtesy of the goals they scored in the 2-2 draw at the Mestalla, will meet Liverpool in the semi-finals in two weeks time.
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