The former striker took charge of the club on a temporary basis over the past few weeks, after the sacking of Erik ten Hag.
Van Nistelrooy may also be leaving United in the coming days, with new boss Ruben Amorim bringing in his own coaching staff.
"It's been a big part, obviously, he felt that everyone was a little bit down," revealed Fernandes after victory over Leicester City. "Results, everything that succeeded with the manager. He understood that the momentum of the players is not great. The mood was down, the confidence was down, so everything he did every day in training, it was trying to bring joy to the training.
"You know, like trying to bring smiles, trying to be involved, tried to make everyone enjoy it, and make it look a little bit loose, the training. And he brought a lot of energy from that, you know, he brought people fighting, training, running, trying duels and lots of small games, competitions, and that.
"Probably going forward, you needed to do more tactics and whatever," he added.
"For him, in the moment, (it) was just he did it, to be honest, and the training has been really enjoyable. Everyone is feeling like they enjoying the training because he was just bringing that extra joy to the training.
"And I like (that), with small things with small games, just to bring the energy back. And he did it. He did it well. And we said it before the game, we don't know what's going to happen to Ruud and the rest of the staff.
"We don't know who’s going to stay, who doesn’t, and we said it before the game. If this has to be one last dance, it has to be a proper one, because they deserve it for everything they did for us."