The Greek defender has spent this season on loan with the Bundesliga club and Allofs has now confirmed that they have activated an option to sign him permanently.
"The contractual details have been resolved 100% and we have taken our option on him." Allofs told Radio Bremen.
"Sokratis will be playing for Werder Bremen in the coming years."
Sokratis has played a total of 29 games for Bremen this season and his commitment to the club is a boost at a time when several of their players have been linked with moves away from the club.
Goalkeeper Tim Wiese has already announced that he will not be extending his contract while Claudio Pizarro has turned down a contract extension and, along with unsettled defender Naldo, he seems set to leave the club this summer.