Pernia was adjudged to have fouled the Reds' captain Steven Gerrard in an aerial collision in the box in the 94th minute of a game Atleti had led from the first half through a goal from their own captain Maxi Rodriguez.
Gerrard stepped up to convert the spot-kick and in the process deny the Spanish side a place in the last 16 of the competition.
But Pernia insisted he did nothing wrong and that the assistant referee admitted his mistake.
"It was a very ugly decision by the linesman, but we all make mistakes, us players too, and I think the linesman made one here," he said.
"In nobody's eyes was that a penalty. We're very hurt to have drawn the game in what was practically the final minute.
"It was an inexistent foul, Gerrard threw himself on top of me. It couldn't have been more clear.
"The linesman said 'sorry, sorry' after the penalty was given. He had time to correct it and go back on it but he didn't."