Keyes also resigned from the company's board.
Toshifumi Suzuki, chairman and CEO of SEJ, has been named acting president and CEO of Dallas-based 7-Eleven until a replacement is found for Keyes.
Keyes has been with 7-Eleven for more than 20 years, holding positions as chief financial officer and chief operating officer. He has been CEO and president since 2000.
Tokyo-based SEJ made a tender offer for the U.S. convenience store chain of $37.50 a share, or about $1.4 billion.
The buyout has taken 7-Eleven private, but 7-Eleven has said it will continue with plans to move its headquarters to downtown Dallas, and will continue to be a Dallas-based company.
7-Eleven (NYSE: SE) operates or franchises about 5,800 stores in the United States and Canada and licenses about 23,200 7-Eleven stores in 17 countries and U.S. territories throughout the world.