The 18-year-old featured eight times in the fourth tier of German football for Bayern’s reserves last season, but he is yet to make a senior Bundesliga appearance after joining from Augsburg.
A nominal fee was paid for Husic as Bayern have a buy-back clause of a reported one million euros should they wish to re-sign him.
The Germany under-18 national spoke of his delight at completing the move and is now looking to prove himself at the Weserstadion.
"It’s a really, really great feeling to be here and to have signed my first professional contract," he told Werder’s official website.
"I am very much looking forward to the task with Werder Bremen."
Meanwhile, club director Frank Baumann sang the praises of Husic and says that he will not just be confined to the youth team as they look to bring him on as a player.
"Raif Husic is a very talented goalkeeper and he will have the chance to develop further still with us," he said.
"Although he is eligible for the under-19 team, we intend to use him in the under-23 side and give him the opportunity to train regularly with the first team."