Juan Mata chose to take their spotkick, which was saved, ahead of the goal-shy striker.
Di Matteo said: "Fernando had a great game, fantastic game. Yes, he missed a chance but other players missed chances too. He had a fantastic game.
"In terms of the penalty, to be honest, that's the players' decision on the pitch.
"I was far away. We had two penalty takers but the players have to take that decision."