Sousa, 42, moved to Maccabi from Hungarian side Videoton.
He previously coached the Portuguese Under-16 national side and had stints in England over a three-year stretch with Queens Park Rangers, Swansea City and Leicester City.
As a player, Sousa was a midfielder for Benfica, Sporting, Juventus, Borussia Dortmund, Inter Milan, Parma, Panathinaikos and Espanyol and made 51 international appearances for Portugal.
He replaces Spaniard Oscar Garcia who left Maccabi at the end of last season for personal reasons.
Garcia, formerly the Barcelona youth team coach, was recruited by Maccabi technical manager Jordi Cruyff at the start of last season and led the perennial underachievers to their first league title in ten years.