Terms of the deal were not disclosed, per team policy.
Biyombo averaged 4.8 points, 6.4 rebounds and 1.5 blocks in 64 games last season with the Charlotte Hornets. He also ranked 17th in the NBA in blocks.
"Bismack brings athleticism and interior length to our team," said Raptors president and general manager Masai Ujiri. "He has proven to be an exceptional rim protector and his physicality will be a great asset to us defensively."
The six-foot-nine Democratic Republic of the Congo native is one of six African-born players currently in the NBA.
Biyombo was drafted seventh overall in the 2011 NBA draft by the Sacramento Kings.