The spot-kick, which Lionel Messi missed but then turned in, proved crucial in equalling the scores going into half time.
"The [problem with the] penalty, aside from the fact that weighing up a refereeing decision is always difficult, is the moment in which it came," Valencia boss Gracia said.
"Going into the break having conceded really hurt us."
In terms of analysing the match, Gracia felt his side deserved more from their performance.
"Justice doesn't exist in football," he added. "The result is what matters. After this game, I'm proud of my players.
"In the first half, we maybe could've done more. In the second, they scored a goal against us when we could've scored with [Denis] Cheryshev's chance.
"It goes to show the personality of the team again. We came here trying to win and you could see that on the pitch."