The 25-year-old, who was born in Johannesburg but developed through the famed Sporting Lisbon academy, will lead the second-tier side in their promotion push this campaign.
The defensive midfielder has previously played in the Portuguese top-flight with Marítimo, and had spells with Portimonense and Ermis Aradippou in Cyprus.
Marakis played for the club last season, where he came up against the likes of Luther Singh [Sporting Braga II], Haashim Domingo and Thibang Phete [both Vitoria Guimaraes II].
Uniao da Madeira were in the top-flight in Portugal as recently as the 2015/16 season, when they were relegated.
Madeira is the birthplace of Cristiano Ronaldo, with the local airport now named after the Real Madrid star, who like Marakis was developed at Sporting.