Ecclestone said in a statement released by his Formula One Management at the Italian Grand Prix that the decision ensures "the progress and success of keeping Formula One in Japan over the long term".
"I appreciate that Fuji Speedway accepted this and am very happy that Fuji Speedway and Suzuka Circuit made this possible," he added.
"It also makes me very pleased that we will retain Suzuka as it has supported Formula One for 20 years and the large amount of our fans."
Toyota-owned Fuji Speedway, who hosted the Japanese Grand Prix in 1976 and 1977, returns to the calendar this year for the 15th round of the season on Sept. 30. It is also assured of next year's race.
Honda's Suzuka facility was a favourite circuit with drivers and hosted the Japanese Grand Prix from 1987.