United were upstaged 1-0 by visiting Villa at Old Trafford on Saturday after Fernandes blazed a last-gasp spot-kick over the crossbar.
Villa's Kortney Hause looked to have gone from hero to zero when he followed an 88th-minute headed goal at one end with a handball at the other five minutes later.
However, Fernandes – taking the penalty ahead of superstar team-mate Cristiano Ronaldo – fired over the crossbar as United suffered their first Premier League defeat of the season and third loss in four games across all competitions.
Fernandes missed from the penalty spot for only the second time in his 23 attempts for United in all competitions and for the first time since October 2020 against Newcastle United in the Premier League.