The announcement was made during the team's 2018 presentation in Madrid.
Vinales, 23, finished third overall last season -- his first with Yamaha after switching from Suzuki -- with three wins and seven podium placings.
Italian team mate Valentino Rossi, whose contract runs out at the end of 2018, was fifth.
"I'm really happy that Yamaha and I have extended our contract by two more years. It's great for me and the team that we were able to make this announcement this early on, because it gives us a sense of calm," Vinales said in a statement.
"We know that I will continue riding my M1 for the coming three seasons, so now we can just focus on the actual racing."
The MotoGP season starts in Qatar on March 18.
(Reporting by Alan Baldwin in London, editing by Ken Ferris)
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