The pair teamed up for the action classic in 1986 and Cruise and Scott remained close after filming ended.
The moviemaker, who was reportedly suffering from an inoperable form of brain cancer, tragically jumped to his death in Los Angeles on Sunday (19Aug12), aged 68, and his sudden passing has left Cruise shaken.
He tells TMZ.com, "(Scott) was a creative visionary whose mark on film is immeasurable. Tony was my dear friend and I will really miss him... My deepest sorrow and thoughts are with his family at this time."
Scott's death is currently being investigated as a suicide.
Dozens of celebrities have already spoken out to pay tribute to the icon, including directors Ron Howard and Michael Moore, and Hollywood star Bette Midler is struggling to come to terms with the news.
In a Twitter.com post, she writes, "Tony Scott's suicide, unfathomable. I am stunned."