The third-placed Red Devils headed into Sunday's Old Trafford encounter a place higher than the visitors on goal difference and looking to bounce back from Michael Carrick's first defeat of an otherwise outstanding two months.
Fernandes was, like so often, the architect as the skipper saw his second-half corner headed home by Casemiro, before providing an exquisite pass from which Matheus Cunha restored their lead after surprise starter Ross Barkley had levelled for Villa.
The assists moved the Portuguese magician onto 16 for the season, breaking David Beckham's club record of 15 Premier League assists set in 1999-2000, and was complemented by a late deflected strike by substitute Benjamin Sesko.
United moved three points clear of Villa and increased their stranglehold on a top-four spot as Unai Emery's side recent top-flight wobble continued.