Garnacho came off the bench in the 57th minute of the Premier League clash and was on the scoresheet in the 82nd minute, bending one into the far corner following a pass from Fernandes.
The 20-year-old decided against celebrating his strike, with Fernandes claiming that the youngster has been frustrated by some recent criticism that has been sent his way.
The goal was Garnacho's seventh in all competitions this season, while he also has four assists, with the South American proving to be the club's most impactful player during the 2024-25 campaign.
Fernandes, who made the breakthrough against Leicester in Ruud van Nisterlrooy's final game in interim charge of the Red Devils, claimed that Garnacho believes he has "lost faith from some fans".
Fernandes explains Garnacho's muted celebration vs. Leicester
"It was a good day at work, I have to say. We have a lot of players with big qualities, but people can get too excited after one game and too down after another," Fernandes told BBC Sport after the win over Leicester.
"Garnacho scored a banger but didn't celebrate like he should because he thinks he has lost faith from some fans. I told him people will always moan but lots of people like you and enjoy what you do.
"I told him to celebrate, it was something special. He is a special player, we have difference makers. They are the ones who win us games. We want them to score very game but that isn't going to happen. The Fantasy managers won't be happy with you guys taking that goal off me."
Fernandes hails Van Nistelrooy with Dutchman's future uncertain
Fernandes also paid tribute to Van Nistelrooy, with the club's interim head coach now stepping aside for Ruben Amorim, who will officially take charge of the Red Devils on Monday.
"It was a long time that I wasn't scoring and now goals are coming in the last few games. Another clean sheet was important for us to bring back the fortress we had here. We have to keep doing that and we have to improve," the Portugal international told reporters.
"Ruud van Nistelrooy fills the club, he loves the club, he wants to bring joy to the players. He brought everyone with a smile to the games, he just wanted us to enjoy it. We wanted to say goodbye as a manager for him properly because he did good things for us.
"It's a new era, a new manager means everything changes but what hasn't changed is that this club has to get back to where it belongs."
Van Nistelrooy's future at the helm is unclear, as Amorim is bringing his own staff with him to Man United, and it remains to be seen whether there is a spot in the new coaching set-up for the Dutchman.