The 20-year-old had been on loan at Granada, but it was announced over the weekend that his spell with the La Liga outfit had come to an end ahead of the expected switch to Benfica.
According to the Manchester Evening News, the Primeira Liga outfit have an obligation to purchase the full-back if he makes a certain number of appearances this season.
The report claims that Benfica also have a separate buy option if he does not feature in the required amount of matches, while Man United have a buy-back option and sell-on clause.
"Manchester United full-back Alvaro Fernandez has signed for Portuguese giants Benfica on loan until the end of the season," read a statement on the English club's official website.
"Although he is yet to play a competitive first-team game for us, Alvaro started four of United's pre-season games, setting up Marc Jurado's goal in the friendly against Wrexham in San Diego.
"This will be another valuable opportunity for Fernandez to get senior experience under his belt and we wish him the best of luck at the Estadio da Luz."
The defender played 14 times for Granada before his loan spell came to an end, with 13 of those appearances coming in Spain's top flight.
"My stay in Granada was special but not as long as we all hoped," Fernandez posted on his official Instagram account after his loan spell with the La Liga team came to an end.
"It was a real pleasure to represent this club and I will always be grateful to the fans and the club in general, but above all to the people who spend day to day with me taking care of me and supporting me since day one.
"We wanted the season to be more successful, but we shared some amazing memories and I will always remember my time at the club as an important part of my career.
"I wish them all the luck for the rest of the season. I know this group and our loyal supporters have the attitude and the fight to stay on our feet this season and meet the goal."
Fernandez spent last season on loan at Preston North End, making 42 appearances for the Championship outfit, but he is yet to make his first-team debut for Man United.
There is no confirmation of how much Benfica could sign the Spaniard for permanently, but Record recently reported that the price is likely to be around €7m (£6m).