Associate Medical Examiner Kenneth Hutchins listed "boat crash" as the cause of death and also said Fernandez was legally drunk with a blood-alcohol concentration of .147.
Fernandez, 24, suffered blunt-force injuries to the head and torso, along with skull and jaw fractures when the boat he was in hit a jetty near Miami Beach in the early morning hours of September 25.
Fernandez and two friends, Emilio Jesus Macias and Eduardo Rivero, were found dead later that morning after their boat was discovered near South Pointe Beach on Government Cut.
Coast Guard personnel on patrol noticed the vessel upside down on the north end of a rocky jetty shortly after 3:15 a.m.
Authorities have not determined who was piloting the boat, which Fernandez owned.
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.
Authorities are conducting a homicide investigation.
A native of Santa Clara, Cuba, Fernandez 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