"He was a creative visionary whose mark on film is immeasurable," Cruise said in a statement. "My deepest sorrow and thoughts are with his family at this time."
Scott died Sunday after jumping from the Vincent Thomas Bridge into Los Angeles Harbor. He was 68. Authorities are investigating the death as a suicide.
Also read: Tony Scott Death: Hollywood Reacts
Cruise and Scott famously collaborated on the 1986 aviation drama, which became one of the biggest hits of the 1980s. In 1990, they reteamed on the race car film "Days of Thunder," which was a box office success, though not on the level of "Top Gun."