The Portuguese midfielder blasted his 93rd-minute spot-kick over the bar minutes after Kortney Hause's late headed goal, which earned Villa their first win against United since December 2009.
United drew a blank for the first time this season despite boasting the league's best attacking record and a star-studded line-up featuring Cristiano Ronaldo, Fernandes, Paul Pogba and Mason Greenwood. Jadon Sancho, Anthony Martial and Jesse Lingard -- last week's match-winner at West Ham -- were unused substitutes and Edinson Cavani only entered the fray with eight minutes remaining.
Hause beat Cavani at the near post at a corner to give Villa the lead in the 88th minute before conceding a penalty for handling a Cavani header. But Fernandes -- on spot-kick duty ahead of Ronaldo -- missed in a dramatic finish to the game.