Hughes has an incentive clause in his contract that will kick in if he reaches 210 innings pitched this season, but he was at 209 2/3 when a lengthy rain delay forced him from Wednesday's 2-1 win over the Diamondbacks, which was his last scheduled regular season start.
Twins manager Ron Gardenhire said he was prepared to let Hughes pitch out of the bullpen before the season ends on Sunday, but Hughes declined.
"I just didn't think it was right," Hughes said before Minnesota's 4-2 loss to Detroit. "If I were fighting for a playoff spot, I'd 100 percent be available. But given the circumstances, I don't think it's the right thing to do.
"I owe too much to this organization for the next two years to risk getting hurt for an incentive. For whatever reason it wasn't meant to be. There's a lot bigger problems out there. I'm proud of my season."
Hughes signed a three-year, $24 million deal with the Twins in the offseason and has already made more than $22 million in his career, according to Baseball-Reference.com. He also cashed in on $250,000 bonuses for reaching 180 and 195 innings.
The 28-year-old is 16-10 with a 3.52 ERA this season, his first with the Twins after seven with the Yankees. The 2010 AL All-Star is 72-60 with a 4.32 ERA in his career.
- Chris Mascaro