Fernandez was a finalist with left-hander Rich Hill of the Dodgers and shortstop Jean Segura of the D-backs. The awards were announced on MLB Network.
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Fernandez was winding down one of the greatest seasons by a starter in Marlins history. The right-hander was 16-8 with a 2.86 ERA, and he shattered the franchise's record for strikeouts in a season with 253.
Fernandez finished second in the NL in strikeouts and first in the Majors, among qualifying starters, with 12.49 strikeouts per nine innings.
In October, Fernandez won the Sporting News Comeback Player of the Year Award.
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From the moment Fernandez broke into the big leagues at age 20 in 2013, he became a sensation. Armed with a 95-plus-mph fastball and a wipeout starter, the Cuban-born right-hander dominated big league hitters.
On a 100-loss Marlins team in '13, Fernandez went 12-6 with a 2.19 ERA. He was named the NL Rookie of the Year by the Baseball Writers' Association of America.
But in May 2014, Fernandez underwent Tommy John surgery, and he missed about 14 months before returning on July 2, 2015. He made just 11 starts and logged 64 2/3 innings that season.
This was his first full season back from surgery, and Fernandez re-emerged as one of the elite right-handers in the game, achieving All-Star status for the second time.
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Fernandez's tragic death has the Marlins' organization and its fans still mourning.
A number of MLB players in the postseason sported either Fernandez's initials or his No. 16 on their caps. The list included fellow Cuba native Aroldis Chapman, who displayed "JF 16" on his hat.
Fernandez's death also has the Marlins surveying the free-agent and trade markets for starting pitchers.
"We're not going to replace him," president of baseball operations Michael Hill said at the General Managers Meetings in Scottsdale, Ariz. "There's not 28 aces in the game."