The US Coast Guard said Fernandez was one of three people killed in the crash on Sunday, off Miami Beach, Florida.
The club said it was "devastated". Marlins's home game against the Atlanta Braves on Sunday was cancelled.
Fernandez was born in Santa Clara, in Cuba, and defected to Florida when he was 16, after three failed attempts. He made his debut for the Marlins in 2013.
Miami-Dade Fire Rescue Chief Todd Garofalo told local news station WSVN: "They found a boat that was up against the jetties. They did do an initial search and they found three victims - two on top of the water, one underneath the boat and they had unfortunately passed away."
We are stunned and devastated by the tragic news that Jose Fernandez, 24, has died in a boating accident. https://t.co/QIBcnIYJ1i pic.twitter.com/SDZoL6NMEb— MLB (@MLB) September 25, 2016
Carlos Martinez drew an 18 for Oscar Taveras and a 16 for Jose Fernandez before he took the mound. Chills man chills pic.twitter.com/7OVKxItE3N— Kent (@RealKentMurphy) September 26, 2016
Heavy heart tonight thinking about Jose Fernandez and those who care about him. Such a loss.— Edgar Martinez (@11EdgarMartinez) September 26, 2016
"Trust me it's not my time yet"- 1 of last texts Eddy Rivero sent before dying on boat w/Jose Fernandez. Story @ 11. pic.twitter.com/y6aTNZVTVs— Erica Rakow (@EricaRakow) September 26, 2016
Receive Instant News Update Via BBM: D3EDEFDF...Click HERE for Details. Share your story with us: email@example.com PLACE YOUR TEXT ADVERT BELOW:>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> How I TOTALLY Got Rid Of my POT BELLY,excess Fat and Overweight In just 2weeks.. Click HERE for Details. Warning To Men: This 3 Foods Is Killing Your Erection. Click Here To Know Them"Trust me it's not my time yet"- 1 of last texts Eddy Rivero sent before dying on boat w/Jose Fernandez. Story @ 11. pic.twitter.com/y6aTNZVTVs— Erica Rakow (@EricaRakow) September 26, 2016