Ipswich Town led inside 29 minutes through Leif Davis after Abdul Fatawu skinned Luke Shaw, but Manchester United drew level just before the break when Fernandes finished a scrambled move after Darwin Núñez slipped.
The captain then converted a controversial second - Harry Maguire's shot deflected in off Jacob Greaves despite a handball appeal - before adding a penalty and a third goal, with Bryan Mbeumo lobbing in a fifth. Substitute Chuba Akpom pulled one back in stoppage time, but it barely dented the scoreline.
Michael Carrick was full of praise for how his side responded after going behind.
"It was a good win. It was a really good win in the end. We played some really good football. The biggest thing today was the mentality of the boys to overcome setbacks," he said. "We controlled the game pretty well for the most part. The boys took it on really well and we were fabulous."
On Fernandes, in the same week he collected the PFA Player of the Year award, Carrick added:
"He showed his quality today. Bruno did what he's good at. He's had a big week winning awards. Three goals and a fantastic performance. It's the whole mentality dealing with it and trusting each other.
"Last week didn't go for us and we accept that. Today was a lot better."
On the summer's business, Carrick said: "I think we've done some fantastic business and we've done it very well with the money we've spent. The spirit is good and they want to fight for each other."
Ipswich boss Gary O'Neil felt his side's collapse hinged on a cruel spell either side of half-time.
"If you look at the last half hour, Man Utd created a lot of chances. The slip for the goal was unfortunate, we were in control and we lost our striker at half-time. Then a massive deflection and handball. You find yourself 2-1 down," O'Neil said.
"The third goal was poor stepping out. Proud of the players to keep going and get a goal at the end. It's a loss at Old Trafford for a newly promoted side."
On the disallowed handball debate, he added: "It doesn't feel like a goal. It feels like it should be chalked off but we accept that it isn't and that's the rule."
Fernandes reflected on a whirlwind week that ended in style.
"We were in control of the game and then conceded the goal, lost a bit of control after that but then got back into the game, scored just before half time and in the second half we were brilliant," he said.
"It is a great accolade for myself but it is together with the team because I couldn't do any of that without them helping me. There are certain days you feel it. It is one of those days when everything comes to you and you have to take it."