Fernandes drilled his 11th league goal this season – and his fifth from the spot – into the bottom corner to punish Douglas Luiz’s clip on Paul Pogba and hand United an eighth win in 10 games.
Bertrand Traore’s calm finish underneath David de Gea had deservedly drawn Villa level, cancelling out Anthony Martial‘s stooping first-half header for the hosts.
But Fernandes’ penalty extended United’s hold over Villa – they have now won 32 and lost just one of the past 44 league meetings between the sides – and leaves Liverpool top only by virtue of goal difference.
Afterwards, United manager Ole Gunnar Solskjaer said: “It’s two extra points if we lose at the end. Eric [Bailly] makes a fantastic block. I didn’t enjoy the last ten minutes, we should have played the game out in a better way.
“It felt like a cup final. We need to play our games better when we have the lead.”
“[Aston Villa] have improved massively and they’ve given us chances. We didn’t stop the crosses well enough, but we’ve made some blocks and saves. I’m pleased with the three points.”
On Paul Pogba, he added: “He’s getting better and better. I think he played well today. They are a physical side and Paul’s one of these guys who can get hold of it for us.
“Don’t get me wrong I’m delighted with the three points and the performance, but there’s always stuff to improve on. Those extra two points are important.
“We’ve improved. I think the league and the season is going to be so tight. We’ve just got to keep working and improving as a team.
“Every time you win a game you take one step further. You’ve just got to accumulate the points. They all count the same.
“We’ve got a big game on Wednesday against City, I’m not even thinking [about playing Liverpool] yet.”