On a team that finished 62-100, the Marlins were 18-10 in Fernandez's 28 starts.
Voting for the award is by the MLB Players Assocation.
"I'm pretty excited to get this," Fernandez said in his interview with MLB Network. "I think the fans are going to enjoy this a lot."
On behalf of Fernandez, the MLBPA's Players Trust is making a donation of $20,000 to the Live Like Bella Foundation for childhood cancer.
Fernandez ascended to stardom faster than anyone anticipated. Due to injuries in the rotation, the Marlins rolled the dice and decided to promote the rookie straight from Class A to the big leagues.
In the last week of the season, Miami manager Mike Redmond discussed the improbability of Fernandez's fast rise.
"To think that he was going to start the season in Double-A, and for him to have a chance to be the Rookie of the Year, none of us would have predicted that," Redmond said. "He's been great and an outstanding story. Going forward, you have that front-line pitcher. Not a lot of teams have that. That's huge."
Fernandez received the honor over fellow finalists Dodgers outfielder Yasiel Puig and Cardinals right-hander Shelby Miller.
Miami's young phenom also was nominated for the NL's Outstanding Pitcher Award, which went to Dodgers lefty Clayton Kershaw. Fernandez and Pirates southpaw Francisco Liriano were the other finalists.
Monday's award was Fernandez's second top rookie honor in recent weeks. Last month, he received the honor from The Sporting News.
The next key date for Fernandez comes on Nov. 11, when the Baseball Writers' Association of America announces the NL Rookie of the Year.
The 14th overall pick in the 2011 First-Year Player Draft made his MLB debut April 7, and he was a force in the rotation until he was shut down after beating the Braves on Sept. 11 due to an innings limit.
The right-hander also was Miami's lone All-Star representative. Even at the Midsummer Classic he was impressive, striking out Dustin Pedroia and Chris Davis while retiring Miguel Cabrera on a soft popout to first in his lone inning.
"When you make guys look silly up there, almost like they don't want to get in the box their second or third time, it's fun to watch," Marlins outfielder Giancarlo Stanton said earlier this season.