Fernandez, 24, and two friends were killed in a boat crash off South Beach early Sunday.
"I think the most important thing is that he brought this community together around our game in a way that we haven't seen with an individual player in a very long time,"?MLB commissioner Rob Manfred told ESPN's Pedro Gomez outside the Mass.
"Obviously, this is a tremendous loss for Jose's family, for the Marlins organization, but really for all of baseball. He was that important to the game. He had an infectious way about him ... the way he played the game on the field, and I think people found that enthusiasm to be just really appealing."
Manfred, Marlins executives Tony Perez and Andre Dawson, and singer Marc Anthony were among about 300 mourners attending the Thursday afternoon service, where he was remembered as a larger than life figure.
"Jose was too good for this league," the Rev. Jose Alvarez said. "He's going to a higher league."
"He loved the water, he loved his boat. It was his vehicle to freedom, his passion," said Boras, who broke down several times during his speech. "It was his dream to canvass the world on his boat.
"He felt free, truly free when he got on his boat after he pitched a game. His two most passionate places were on the water and on the mound.
"Ironically the waters that brought Jose to us were the waters that brought Jose to a new freedom: the high heavens."
The private service lasted more than two hours. Pallbearers wore black Fernandez jerseys as they carried his casket.
After the service, Marlins players were set to fly to Washington, D.C., to play in their final series of the 2016 season.
On Wednesday, Marlins owner Jeffrey Loria, manager Don Mattingly, hitting coach Barry Bonds and players including Ozuna?and Giancarlo Stanton wore white T-shirts emblazoned with Fernandez's image and the letters "RIP" as they slowly walked the hearse away from Marlins Park in Miami's Little Havana neighborhood. Many in the crowd of about 1,000 chanted "Jose! Jose!" and some waved Cuban flags in honor of Fernandez's heritage.
Hundreds of fans streamed into St. Brendan's Catholic Church later Wednesday for a public viewing, which was scheduled to last into the night. Many said they felt compelled to come, not only because of Fernandez's popularity as a player, but also because he was a hero to many in the Cuban-American community.
Inside the church, mourners filed past a closed casket framed by flower arrangements in the shapes of the U.S. and Cuban flags, with a large family photo of Fernandez off to one side. Many touched the casket lightly and crossed themselves.
The cause of the crash is being investigated by the Florida Fish and Wildlife Conservation Commission. In addition to Fernandez, Emilio Jesus Macias, 27, and Eduardo Rivero, 25, also died in the crash.
Fernandez was an emerging baseball star known for his exuberant personality and style of play. He was National League Rookie of the Year in 2013 and a two-time All-Star. This year, he set a single-season Marlins strikeout record with 253.
On Thursday, officials in Tampa said that a jersey worn by Fernandez in high school was missing after a candlelight vigil at his former high school. Officials at Alonso High School filed a police report, and authorities are asking whoever took the jersey to return it.
Information from The Associated Press was used in this report.