There were moments of silence before every game and tributes of all fashions on Sunday for Fernandez, whose infectious enthusiasm made him immensely popular with teammates, peers and baseball fans.
"When you watch kids play Little League, that's the joy Jose played with," said Marlins manager Don Mattingly, breaking down in tears during an emotional news conference attended by all of Fernandez's teammates.
The Marlins' game against the Atlanta Braves scheduled for Sunday afternoon in Miami was cancelled.
The 24-year-old was one of the biggest rising stars in the league. He was a Cuban refugee who became a US citizen and achieved his dream of starring for a team in Miami which is considered the cultural heart of Cuba in America.
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"All of Baseball is shocked and saddened by the sudden passing of Miami Marlins pitcher Jose Fernandez," said MLB commissioner Rob Manfred.
"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. Our thoughts and prayers are with his family, the Miami Marlins organization and all of the people he touched in his life."
Fernandez was one of three people killed in the accident, in which the 32-foot vessel had a "severe impact" with a jetty, according to the authorities. The Coast Guard discovered the overturned boat around 3:30 am (07:30 GMT).
The boat carrying Fernandez and two others was travelling at a high speed when it slammed into rocks, authorities said. Fernandez did not drown but rather was killed as a result of the impact, officials added.
Fernandez announced on Instagram last week that his girlfriend is pregnant.
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The New York Mets hung a jersey with Fernandez' name and number 16 in the home dugout at Citi Field. MLB players openly mourned the loss of Fernandez taking to social media to express their deep feelings.
Absolutely devastated hearing about Jose. Thoughts and prayers go to his family, friends, and Marlins org.
— Mike Trout (@MikeTrout) September 25, 2016
Bryce Harper of the Washington Nationals wrote:
Absolutely crushed and shocked at the news about Jo-Fez..My thoughts and prayers go out to his family, friends, and the @Marlins org!
— Bryce Harper (@bryceharper3) September 25, 2016
Fernandez was originally scheduled to start on Sunday, but on Saturday the team announced he would skip that start and pitch Monday's opening game of a series against the New York Mets.
Fernandez was enjoying his best major league season, posting a 16-8 record with a 2.86 earned run average.
The hard-throwing right-hander set a club record with 253 strikeouts this season, and his 12.49 strikeouts per nine innings led the majors.
After three unsuccessful attempts, Fernandez managed to leave Cuba for Florida at the age of 15. He was thrown in jail after getting caught on the third attempt.
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On his final attempt he had to dive into the water to rescue his mother after she had fallen overboard.
Fernandez was a first round draft pick and received a $2 million signing bonus.
At 20, he broke into the major leagues and was National League Rookie of the Year in 2013.
In May of 2014, however, he underwent Tommy John ligament replacement elbow surgery. He returned to the major leagues on July 2, 2015, and the same year became a US citizen.
Fernandez's last start, on Tuesday, was one of the best of the two-time All-Star's career. He tossed a season-high eight innings and struck out 12 in a 1-0 shutout win over the Nationals.
The NFL's Miami Dolphins joined several other professional sports teams by holding a moment of silence for Fernandez before their game against the Cleveland Browns.
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