The 27-year-old frontman was a pivotal figure as Alaves beat relegation from the Segunda Division by a single point last season.
In fact, his 25 goals saw him end the season as the division's top goalscorer, ahead of Murcia's Kike and Stefan Scepovic of Sporting Gijon.
A Bilbao statement on Friday read: "Athletic Club, Deportivo Alaves and Borja Viguera signed today, Friday June 13, an agreement so that the player can join our club .
"Viguera has signed a contract until June 30 , 2017 and his termination clause will be €30 million."
Viguera, who formerly played for Real Sociedad, is set to be unveiled by the club later on Friday.
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