Fernández, who was 24, and two other men were found dead after their boat was discovered at the entrance of Miami Harbor, said Florida Fish and Wildlife Conservation Commission spokesman Lorenzo Veloz.
Coast Guard personnel on patrol noticed the vessel upside down on the north end of a rocky jetty shortly after 3:15 a.m., Veloz said at a news conference.
Divers recovered two bodies under the boat, and a third victim was found on the rocks. The names of the two other victims -- also in their 20s -- are being withheld until relatives are notified. The men were Fernandez's friends, Veloz said.
Veloz said Fernández's death was a loss to Miami, to baseball and to anyone who ever met him.
"He was pillar to our community. He was involved in everything that he could be to give back," Veloz said. "I had the experience of talking to him several times -- down-to-earth, great person ... I'm sorry I'm getting goosebumps right now. It's really hitting home and it's horrible."
Based on impact evidence and the severity of damage, officials concluded the boat -- a 32-foot SeaVee center console model -- hit the rocks at full speed, Veloz said.
Top speed on the boat would be between 50 mph and 65 mph, depending on the engines with which it was equipped, according to SeeVee's website.
Fernández was a passenger on the boat, and was not the owner, Veloz said.
"The boat is a total loss right now from what we can see," Veloz said. "It's horrible, it's bad, it's bad."
Drugs and alcohol did not appear to be factors in the accident, he said, but he added that investigators had been been unable to get under the overturned wreckage. Autopsies have not been conducted. None of the three victims was wearing a life vest, he said.
Emotional news conference
"The magnanimity of his personality transcended culture, religion and race, I mean it just did," Marlins President David Samson said at a news conference where he was flanked by the team and other officials. Several people appeared visibly shaken.
"Jose is a member of this family for all time," Samson said. "His story is representative of a story of hope, and of love and of faith, and no one will ever let that story die."
The Marlins' game against the Atlanta Braves on Sunday was canceled, Samson said.
"When you watch kids playing Little League... that's the joy that Jose played with -- and the passion he felt about playing," said Marlins Manager Don Mattingly, stopping midsentence to wipe away tears. He appeared too emotionally shaken to continue.
Fernández was born in Santa Clara, Cuba, and defected to the United States in 2008.
Drafted by the Marlins in 2011, he went on to become the franchise's star pitcher, named National League Rookie of the Year 2013 and a two-time All-Star.
Saving his mom
But his story is about more than baseball accolades, and Mattingly certainly isn't the only person to shed tears over Fernández's death. The oft-smiling Fernández had many friends in the game, owing to his cheerful demeanor and fierce competitiveness.
He also owned what Miami Herald sportswriter Dan Le Batard once called a "rags to pitches" story that many, especially those in Florida's Cuban-American communities, found inspiring.
In 2008, Fernández made his fourth attempt to flee Cuba, according to a 2013 Miami Herald story
. He'd been jailed for a previous failed attempt and, this time, was attempting to reach America, via Mexico, with his mother and sister.
Once on the open water, the newspaper reported, someone fell off of the boat, and Fernández, a good swimmer, asked no questions; he jumped in to save the person. It turned out to be his mother, Maritza.
"I dove to help a person not thinking who that person was. Imagine when I realized it was my own mother. If that does not leave a mark on you for the rest of your life, I don't know what will," he told the Herald.
Once in the United States, Fernández had trouble adjusting. Fifteen at the time, he missed his grandmother, Olga, desperately, Le Batard wrote in a 2013 profile
Back home, he was "really, really poor," Fernández told his fellow Cuban-American Le Batard, and he was happy to make $4 a day selling tomatoes and onions.
In the U.S., the simplest things, such as computers and motion-activated faucets, eluded him. He wrote phone numbers down in a book because he didn't realize his phone would store them, the profile said. His grasp of English didn't extend much beyond curse words.
But there was one language besides Spanish that he understood perfectly: baseball. As a high school sophomore, Fernández threw 94-mph fastballs, as fast as some pros, and he led Braulio Alonso High School to two state championships, Le Batard reported.
The Marlins selected him in the first round of 2011 Major League Baseball draft, and he first took the mound for them in April 2013 en route to National League Rookie of the Year honors.
It was after that season -- when Fernández told Le Batard how much he missed Olga, who had climbed to her Santa Clara roof with a radio to catch the Marlins games when Fernández pitched -- that the Marlins arranged a surprise.
A heartwarming reunion
While he conducted an interview in the Marlins locker room that ventured into the topics of his mother and grandmother, whose names he has tattooed inside his bicep, the interviewer asks Fernandez what Olga would tell him if she were there in Miami.
"I don't think she would be here," he replied, his sadness evident in his eyes.
Little did he know that Olga had arrived in Miami a half hour prior. The Marlins had arranged for her visa. As Marlins owner Jeffrey Loria escorts Olga into the locker room, Fernández beams a boyish grin, clearly in disbelief.
He says only, "Oh," as she rushes over to him. His face is bright red as Olga embraces him for the first time in six years.
"Oh my God," he says, almost as if he's exhaling. "You've got to be kidding me."
"You look so great, papi. You look so great," Olga tells him in Spanish as he clutches her, kissing the top of her head.
Jeffrey Loria explained the team's motivation in getting Olga to the United States.
"Having watched the dynamic unfold with him, caring about his grandmother so much, it kind of came to our attention here. We have a big family here in this organization and there was a link missing in that family so we closed the gap. We got her here," he said.
Baseball world stunned
News of his death sent shockwaves through the baseball community, with players and fans alike taking to social media to express their grief.
"We are stunned and devastated," Major League Baseball said in a statement.
"I've never met anyone who extracted more joy, more passion out of what he did than José Fernández," baseball analyst Buster Olney said on ESPN. "When you watched him pitch, he loved it so much. He had so much emotion."
"He's sort of the American dream for the Cuban baseball player," Le Batard said. "This kid is a symbol for Cuban life and the things that can be accomplished in this country."
Former MLB pitcher Dan Haren tweeted: "Jose Fernandez is one of the most genuine guys I've ever played with. He loved life, he loved baseball... he will be missed dearly."
Major League Baseball Commissioner Rob Manfred issued a statement saying, "He was one of our game's great young stars who made a dramatic impact on and off the field since his debut in 2013."
Many fans spoke of their sadness that, having already achieved remarkable sporting success, Fernández's life had been cut short just as he was starting a family.
Five days ago, the young star had posted a picture to Instagram of his pregnant girlfriend, with the caption: "I'm so glad you came into my life. I'm ready for where this journey is gonna take us together."
Baseball fan Matt Birnbach wrote: "Jose was a reason you watched baseball. He was must-see TV and his personality is what made him great. Absolutely crushed right now."