The 24-year-old Spaniard was with East Fife last season and impressed during a short trial at Dens Park.
Etxabeguren spent five years with Real Sociedad and was included in their Champions League squad for season 2013-14.
Following his switch to Scottish League Two in January, he made 15 appearances for the New Bayview club.
Dundee have signed defender Julen Etxabeguren Leanizbarrutia on a three-year deal.