Fernandes pounced six minutes before half-time after Emiliano Martinez had turned Marcus Rashford’s shot into his path.
United midfielder Casemiro also hit the bar and curled a second-half effort just wide.
However, Ezri Konza nearly scrambled a close-range equaliser from a late corner that had been flicked on at the near post, but the Villa defender was unable to adjust his body position quickly enough to steer the ball goalwards and United were able to clear.
The result ensures United have a healthy advantage on the clubs chasing a top-four spot, with Villa now nine points adrift of the Red Devils having missed the chance to cut the gap to just three points.