Hernandez (13-12) was scheduled to pitch the Mariners' final game Sunday, but general manager Jack Zduriencik decided rest would be best for the 24-year-old Venezuelan.
"Is one more outing going to make that much of a difference?," Zduriencik said of the Cy Young voting for the American League's top pitcher.
"In my opinion, he should get the Cy Young. He's earned it regardless of what the won-loss record is."
Hernandez said he was disappointed with the decision.
"I just want to pitch," Hernandez told reporters. "I said, 'You know, Jack, I want to pitch,' but he's the boss. He made the decision."
The right-hander leads the AL in three major categories and is tied for first in another.
He has the league's lowest earned run average (2.27) and leads the AL in strikeouts (232), innings pitched (249.2) and is tied for most starts (34).
Despite the sterling numbers, Hernandez's won-lost record may hurt him in Cy Young voting, and he has received little support from the Mariners, who at 61-98 have the AL's worst record.
(Reporting by Gene Cherry in Salvo, North Carolina; Editing by Steve Ginsburg)