Fernandes, who can also operate as a forward, was a member of the Benfica squad last season that won the Portuguese Primeira Liga title.
The 21-year-old has also played twice for the Portugal senior team after making his debut in 2018 and has made more than 60 appearances for various age group teams, winning the Under-17 Euros in 2016.
The transfer could pave the way for the potential departure of Christian Eriksen - who has been linked with a move to Serie A side Inter Milan - before his contract expires at the end of the season.
Spurs, eighth in the league standings, travel to Watford on Saturday. (Reporting by Rohith Nair in Bengaluru; Editing by Alex Richardson)