The 27-year-old topped the scoring charts in Spain's Segunda Division last season with 25 goals, a return that accounted for nearly half of those netted by Alaves in the entire campaign.
Athletic announced the deal on their official website on Friday as Viguera underwent a medical at the San Mames.
"Athletic Club and Deportivo Alaves have signed an agreement for Borja Viguera to becoming the latest player at our club," a statement read.
"Viguera has signed a contract until 30 June 2017 and will have a clause of 30 million euros."
The transfer will see a return to La Liga for the striker, who has not featured in the top flight since he made a handful of appearances in 2010 for Real Sociedad.