The 25-year-old heads back to the country of his birth, as he prepares for a second successive season on loan in La Liga.
He spent the 2017-18 season with Malaga, as the side got relegated in horrific fashion, finishing 23 points adrift of safety. Borja only managed two goals in his 16 appearances during his season-long stay.
He now heads to Alaves, who finished 14th last season. The former Atlético Madrid striker will be hoping to improve his form in order to seek a resolution to the disappointing time he has had at Swansea since his arrival at the south Wales club in 2016.
Borja has experience at international level, having represented Spain at Under-17, Under-18 and Under-19 level. He will be hoping to improve his performances in La Liga, as he bids to catch the eye of new Spain manager Luis Enrique.
Meanwhile, Swansea have confirmed that the club have sold central defender Kyle Bartley - who has joined Championship rivals West Brom on a three-year deal.
Speaking after making the move to the West Midlands, Bartley said: "“After speaking with Darren I knew this was the place I wanted to be be. He let me know his ideas for the season and the next few years, his ambitions for the club and he told me about the fan base and the facilities. I’m hoping to be involved quickly.”