The Spanish centre-half, 25, has put pen to paper on a four-year contract which will see him stay at the club until 2020, ending weeks of uneasy speculation about his future.
Family man Ayala never looked elsewhere
The PFA Championship Fans’ Player of the Year told the club's official website that he never had any intention other than to stay at the club, saying "I only had one decision in my mind and that was to stay".
He also had praise for manager Aitor Karanka, saying that he had improved as a player under the former Real Madrid centre-half, and expressed his gratitude for the support of the fans.
Ayala admitted that the chance to play in the top flight for Boro was "a dream come true", and that the squad were hopeful for a good season after an impressive transfer window.
While the former Liverpool and Norwich City man does not use social media, his partner Hannah O'Neill tweeted: "Of course he was always staying... One baby born in the Boro... Need the next one to be born here too!"
Ramirez and Guzan moves confirmed
The news came shortly after the announcement that summer signings Gaston Ramirez and Brad Guzan have both received the necessary paperwork required to play for Middlesbrough in England, after their recent summer moves.
Ramirez rejoins after a loan spell with the club last season when he inspired Boro's faltering promotion bid, while Guzan arrives as another goalkeeping option alongside two of Victor Valdes, Dimi Konstantopoulos and Tomas Mejias.
Manager Karanka has recently confirmed that one of the two latter goalkeepers is likely to leave the club this summer.