The 24-year-old pitching sensation's fingerprint and DNA were found on the steering wheel, and his DNA was also found on the throttle of the 32-foot vessel named "Kaught Looking," according to the final incident report from the Florida Fish and Wildlife Conservation Commission.
Fernández owned the vessel, which was traveling at about 66 mph when it struck a jetty near Miami Beach in the early morning hours of September 25, according to digital forensic analysis of its GPS units, the report said.
The Marlins pitcher and two friends, Emilio Jesus Macias and Eduardo Rivero, were found dead after the boat was discovered near South Pointe Beach on Government Cut. The three men, who were ejected from the boat during the crash, died from blunt-force trauma and drowning, the report said.
Fernández had cocaine in his system and was legally drunk, with a blood-alcohol concentration of .147, according to the report.
'In a reckless manner'
"Fernández operated ... with his normal faculties impaired, in a reckless manner, at an extremely high rate of speed, in the darkness of night, in an area with known navigational hazards such as rock jetties and channel markers," the report said.
Investigators concluded that Fernández violated a number of state laws, including boating under the influence manslaughter, vessel homicide, and reckless or careless operation of a vessel.
The report also said the fact that Fernandez operated the vessel with the interior blue lights on along with a vinyl windshield enclosure likely interfered with his "night vision capabilities."
The report offers a look into the last hours of one of baseball's premier young pitchers, including a screen shot of a text message from Fernández' girlfriend to one of the men on the boat. She wrote that Fernández was "not in the best state of mind," that they had argued recently and that he was "pushing me out the door."
"I just need you to take care of him," the girlfriend wrote to Rivero.
'It's not my time yet'
A friend of Rivero also posted a photo of text messages he exchanged with Rivero on the night of the accident, according to the report.
In the messages, Rivero's friend urged him to "keep Joe cool" and "keep him close to shore."
"Trust me," Rivero wrote back. "It's not my time yet."
Fernández and his two friends spent an hour and 45 minutes before the crash at American Social bar on the Miami Rivera, where they purchased two bottles of Don Julio tequila and other drinks, according to the report.
Fernández suffered blunt-force injuries to the head and torso, along with skull and jaw fractures during the crash.
At the time of the crash, Macias was standing near the vessel's front center console and Rivero was standing behind the center console seat, according to the report.
The families of Macias and Rivero are each seeking $2 million in wrongful-death lawsuits against the Fernandez estate, CNN affiliate WPLG reported.
Coast Guard personnel on patrol noticed the vessel upside down on the north end of a rocky jetty shortly after 3:15 a.m.
"No matter what the report has concluded, nothing will ever diminish Jose's everlasting positive connection with Miami and the Miami Marlins," team president David Samson said in a statement, WPLG reported.
"Nor can it lessen the love and passion he felt for his family, friends, teammates and all his fans in South Florida and around the world."
A beloved sports figure
Autopsies determined that Macias and Rivero had levels of alcohol below the legal limit in Florida, which is .08. Rivero also had traces of cocaine in his system, the medical examiner's report said.
A native of Santa Clara, Cuba, Fernández was a beloved sports figure in the city where so many of his countrymen have settled and prospered. Drafted by the Marlins in 2011, he rose to become the franchise's marquee pitcher, the National League Rookie of the Year 2013 and a two-time all-star.
His death stunned Miami and the baseball world, where he was a popular figure with teammates
After defecting from his native Cuba at 15, Fernández made his big-league debut against the New York Mets on April 7, 2013.