Fernandez underwent a medical on Tyneside on Thursday before completing a move believed to be worth around £6m. He has signed a two-year deal with the club, where he will hope to establish himself as Jamaal Lascelles' new defensive partner.
Speaking to Newcastle's official website, Fernandez said: "It was a long day but I’m really happy to be here.
"It’s a new challenge in my life and I’m very excited to meet all the players and staff here."
The Spaniard is the second player to leave the Liberty Stadium for St James' Park this summer, following in the footsteps of Ki Sung-yueng, who joined Newcastle on a free earlier this summer.
Fernandez made over 120 appearances for Swansea in four seasons at the club after joining from Napoli in 2014.
Rafa Benitez made no secret of his desire to bolster his defensive options on deadline day, and will be pleased that he has managed to do so. Fernandez becomes the second defender to sign for the Magpies, following the arrival of Fabian Schar.
Newcastle's defensive record was the 7th best in the league last season and Rafa Benitez clearly believes it will be an important area of the team again this year.
Benitez has also added Yoshinori Muto, Martin Dubravka and Salomon Rondon to his squad this summer, but he has had to do so on limited funds due to a lack of support from chairman Mike Ashley.
Fernandez may be part of the squad that faces Tottenham in Newcastle's Premier League opener on Saturday.