Victoriano Sanchez Arminio told reporters referee Cesar Muniz Fernandez probably got it wrong when he ruled Elche midfielder Carlos Sanchez had obstructed Pepe at a 94th-minute corner and pointed to the spot.
The Elche players were furious with the decision, also because the allocated three minutes of added time had already ended and their plucky performance had been rewarded with a dramatic equaliser three minutes earlier.
Cristiano Ronaldo, who had put Real ahead with a 51st-minute free kick, drove the penalty into the corner and a host of angry Elche players confronted Muniz Fernandez on the final whistle.
Television replays showed Pepe and Sanchez grappling with each other before tumbling together to the floor and the Elche players' fury appeared justified.
"I don't think he got it right," Sanchez Arminio said.
"But there you go, sometimes we get it right and sometimes not, that's football," he added.
"When someone is not on form on the pitch it's one thing after the other.
"The best person to ask about it is him (Muniz Fernandez). I don't know how he was feeling, if he maybe had some family issue that meant he wasn't in the right frame of mind."
Muniz Fernandez has already been mired in controversy once this season when he disallowed what appeared a perfectly legitimate goal scored by Sevilla defender Cala against Barcelona at the Nou Camp.
Wednesday's decision prompted an ironic comment from Barca's Spain centre back Gerard Pique, who referred to the match on his Twitter feed as a "comedy film".
Barca president Sandro Rosell was quoted as saying in local media on Thursday he "still couldn't believe it" and "the evidence speaks for itself".
Spanish media reported the referees' committee had decided Muniz Fernandez would not officiate at another Elche match this season.