Hiroshi Soda, president of the Mobilityland Corporation that runs the Honda-owned circuit, said in a statement that a formal contract had been signed after a basic agreement was reached in March.
He thanked Ecclestone for "showing us a great deal of understanding in the process".
Honda are returning to Formula One in 2015 as engine partners to McLaren after quitting the sport at the end of the 2008 season.
Toyota, whose Fuji track hosted the Japanese Grand Prix in 2007 and 2008, pulled out of Formula One at the end of 2009 while tyre supplier Bridgestone quit a year later.
There is currently no Japanese driver in the sport after Kamui Kobayashi, the country's most successful grand prix racer, lost his seat at Sauber last year.
"It has been agreed that the Formula One Grand Prix will be hosted at Suzuka Circuit until 2018," said Ecclestone in Friday's statement issued during the Belgian Grand Prix.
"It is also great to see Honda back in Formula One in 2015. I am sure that the Japanese Grand Prix will attract greater attention than ever."
(Reporting by Alan Baldwin; Editing by John Mehaffey)
