Fernandes put the visitors into a deserved lead on Monday night, only for meek added-time defending to allow Jean-Ricner Bellegarde to score Wolves' first Premier League goal since October 26.
But whatever United manager Ruben Amorim said at halftime did the trick, with Bryan Mbeumo, Mason Mount and Fernandes hitting the target in front of United-supporting world darts champion Luke Littler.
The Red Devils move up to sixth with a win that leaves Rob Edwards' men rooted to the bottom of the standings with just two points from their opening 15 matches.
Wolves fans turned on their players at points during an evening when owners Fosun and chairman Jeff Shi were implored to leave, with many supporters only arriving in the 15th minute in protest.
"Look, I understand the frustration totally," Edwards said of the protest and the potential impact on players.
"I think it's been six months since we've last won, so I get it.
"The players are trying, I can promise that. But there's clearly a lack of confidence and a lack of belief there."
Those home fans in place for kick-off made sure to boo former star Matheus Cunha's every touch.
Wolves conceded a shambolic 25th-minute opener as Andre was dispossessed by Casemiro and Fernandes was allowed to squirm a shot past goalkeeper Sam Johnstone.
The home fans raged and so nearly saw their side concede another minutes later, with Mbeumo denied by Johnstone and Cunha seeing an effort cleared off the line before Amad Diallo volleyed wide.
There were audible groans as Wolves' toothless attack faltered, only for Amorim's retreating visitors to cough up a leveller. David Moller Wolfe had time to hit a cutback from the byline into the ground and stretching Bellegarde struck.
United's players met for a huddle before a second half they played with renewed vigour and was only six minutes old when they went ahead.
A strong Luke Shaw challenge on Bellegarde - one that would force the goalscorer off - started a counter that saw Cunha play in Dalot. Johnstone rushed off his line and the wing-back smartly played the ball across for Mbeumo to direct into an empty net.
The United relief was palpable and another followed in the 62nd minute as Fernandes clipped a brilliant ball into the box for Mount to sweep home.
Yerson Mosquera was then adjudged to have handled a Diallo attempt and, having been sent to the monitor, referee Michael Salisbury pointed to the spot, from which the skipper slammed home in the 82nd minute.
"I think, once again, after we scored a goal we were a little bit sloppy ... and that gave a little bit of hope to the opponent," Amorim said.
"I think the pace, the quality that we showed in the second half, understanding that the moment of Wolves is really hard as a team, as a club, so we took advantage of that."
