The Portugal international delegated the responsibility to Marcus Rashford after the Englishman was fouled in the box, despite being on a hat-trick.
Speaking after the game, Fernandes said: "Of course every player wants a hat-trick. But after the game in the Premier League I told Rashford that he could take the next one so I remembered that and also he's one of the top scorers in the Champions League so it's important for him to get the confidence. It doesn't matter who takes the penalty as long as the team scores.
"We're in a good position but can't relax - we have to think of the Premier League now and win the next game on Sunday and after that we don't have much time but we have some time to think of the next Champions League game."