Scherzer, winner of the award in 2013 while playing for the Detroit Tigers in the American League, joins an exclusive club which includes Gaylord Perry, Randy Johnson, Roger Clemens, Pedro Martinez and Roy Halladay.
Scherzer was the runaway winner for the National League award this year, finishing with 192 voting points, well ahead of second-placed Jon Lester of the Chicago Cubs, who finished with 102 points.
"For the writers to choose me for everything I was able to accomplish this year, I'm so grateful," Scherzer said on the MLB Network.
But the race for the American League Cy Young winner went down to the wire, with Boston Red Sox right hander Rick Porcello edging out Justin Verlander of the Tigers.
Verlander, who led the American League this season with 254 strikeouts, earned more first place votes than Porcello, 14 to 8.
However, two writers did not list Verlander at all on their five-pitcher ballots, skewing the results so that Porcello won 137 voting points to Verlander's 132.
"It's unbelievable," said Porcello, who struggled in his first season with Boston last year before improving dramatically in 2016.
"I don't think I like to admit how difficult it was playing in Boston the first year," the 27-year-old said. "I take a lot of pride in what I do and I think the pressure I was putting on myself -- and obviously there's pressure playing in a city like that -- it's something that I almost couldn't get out of my own way.
"That offseason I was able to kind of regroup mentally, refocus and take things the way I wanted to, and take them slow. Started with my foundation, my delivery, getting back to doing the basics and doing simple better. It worked."