The Malaysian Grand Prix venue has been on the schedule since 1999.
It has drawn increasingly large crowds in recent years, with 125,000 across three days last season and a new record expected this weekend.
Dorna chief Carmelo Ezpeleta said Sepang's growing popularity proved that new markets could be successful.
"To sign this agreement for the next three years is fantastic news for all parties involved in MotoGP," he said.
"The Sepang International Circuit is a great facility that is a favourite for many reasons, and is invaluable on the race calendar.
"It is one of the cornerstones of the championship's push into new markets, and continues to draw ever-greater number of fans. I hope for many more years of exciting racing to come."