He left on a free transfer to Betis last season after his contract with Eibar expired, but has failed to make an impact at the Seville club, appearing in eight league games and failing to score.
Inui joins an Alaves side who have recorded their best ever points total in the first half of a season and sit fifth in La Liga on 32 points, one behind Sevilla in fourth and with hopes of qualifying for the Champions League for the first time ever.
Inui has made 32 appearances for Japan and scored in their 3-2 defeat to Belgium in the last 16 of last year's World Cup in Russia.
He will take the place of Ibai Gomez, one of the key players in Alaves' remarkable season who left the club earlier this month to move back to Athletic Bilbao.
(Reporting by Richard Martin; Editing by Christian Radnedge)
