Daugherty, 33, who lives in South Vienna, Ohio, outplayed, outlasted and outwitted Twila Tanner, 41, in the 39-day contest. Daugherty received five of the seven-person jury's votes.
"Can you believe it?" Daugherty repeatedly asked during an interview with The Associated Press following his win Sunday.
At the start of the game, originally divided by gender, it seemed Daugherty would be the first player to go: His inability to cross a balance beam during an immunity challenge forced his tribe to vote out one of their own. Thirty-nine days and a powerful all-female alliance later, he somehow survived.
"They were the creators of their own demise," Daugherty told the AP about the ballyhooed all-female alliance. "When it got down to me and six women, I stepped back and watched them tear themselves apart."
On the final episode, Daugherty won both immunity challenges. During the season's requisite final endurance challenge, Daugherty successfully held a warrior stance with a bow-and-arrow longer than Scout Cloud Lee, 59, and Tanner, giving him the power to take Tanner with him to the final two.
"That was definitely something I used in my strategy," said Daugherty. "I got somebody like Twila, the most controversial player in the game, with me at the end."
Daugherty works for the Ohio Department of Transportation. Tanner works for the Missouri Department of Transportation.
Toward the end of the game, Tanner pledged an alliance allegiance to Ami Cusack and Leann Slaby by swearing on her son's life but later backed out, infuriating some survivors.
The final tribal council was tearful with players expressing hurt feelings over lies told and friendships broken throughout the game. Julie Berry, who bonded with Daugherty, was particularly upset and told the final two her vote was either "for Chris or against Chris."
"I may have to prove to Julie that I'm worth having as a big brother," Daugherty, who voted her off the island, told the AP. "I think it's amazing. When you go to play this game, you do not factor in emotion. I went to play and win a million dollars."
This ninth edition of "Survivor" has been the most watched reality show currently airing, beating competitors such as "The Apprentice" and "The Amazing Race," according to Nielsen Media Research. But that hasn't stopped some fans from calling the volcano-laden season humdrum because the tribes were gender-divided (a tactic previously seen in the "Amazon" season) and strong alliances predictably plucked off tribe members (older men sent a series of younger men home; women voted off a row of men).
Daugherty said during the finale reunion, a disappointed Tanner had very little say to him, other than a "short 'good job.'"
At the end of the reunion, the location for the 10th season and yet another twist was revealed. Twenty castaways - past seasons have only included 16 or 18 - are headed to Palau, an island nation located in the Pacific. Host Jeff Probst promised "everything the survivors have come to expect will be wiped out in the first 10 minutes."