The signing was announced on the German club's official website on Saturday, with Burki making the switch from the Swiss Super League runners-up.
The 23-year-old is part of the Switzerland squad that will travel to the FIFA World Cup in Brazil, and Freiburg sporting director Jochen Saier said the move was a result of a long-term interest in the player.
"We have observed Roman Burki for a long time and are very pleased that the move has come about," he said.
"He fits in our requirements and has gained experience in the Super League as well as in Europe and for the Swiss Under-21 national team."
Burki himself, meanwhile, was excited about the prospect of joining international team-mates Admir Mehmedi and Gelson Fernandes at Freiburg, who finished 14th in the Bundesliga this season.
"The challenge of the Bundesliga and Freiburg excites me greatly," he said. "Through Admir Mehmedi and Gelson Fernandes the club has a good reputation in Switzerland.
"That to me is a further step in my career and I am looking forward to my time in Freiburg."
