The men were prosecuted for "very grave acts of terrorism" on Tuesday and given several days to appeal the sentences, said a statement read on state television.
The death penalty sentences were upheld both by Cuba's Supreme Tribunal and the governing Council of State and "at dawn today the sanctions were applied," said the statement.
The speed and severity of the punishment underscored Cuba's growing alarm and frustration over a string of successful and attempted hijackings that it blames on what it believes is a lax attitude by American authorities toward hijackers who reach American shores.
Earlier Friday, the government announced that it had frustrated the attempted hijacking attempt of a plane the night before.
The Council of State, which is headed by President Fidel Castro, studied the appeal over several hours, taking into account the seriousness of the penalty recommended, said the statement. The council also considered the "potential dangers that were implied not only for the lives of numerous innocent people but also for the nation's security" when the crimes were committed, it said.
Ultimately, the council decided that "the decisions of both courts were absolutely just and in accordance with law and it ratified the sentences."
The statement identified those executed as Lorenzo Enrique Copello Castillo, Barbaro Leodan Sevilla Garcia and Jorge Luis Martinez Isaac, "the three principal, most active and brutal leaders of the hijackers."
It said another four men received life sentences: Maikel Delgado Aramburo, Yoanny Thomas Gonzalez, Harold Alcala Aramburo and Ramon Henry Grillo.
Also sentenced in the same case were Wilmer Ledea Perez, who received a 30-year term; Ana Rosa Ledea Rios, 5 years; Yolanda Pando Rizo, 3 years; and Dania Rojas Gongora, 2 years.
Capital punishment in Cuba is always carried out by firing squad. It has been used sparingly in recent years.
No one was hurt when the group, reportedly armed with at least one pistol and several knives, seized the ferry in Havana Bay in the earlier hours of April 2 with about 50 people aboard. The captain was ordered to sail to the United States.
Later that day, the ferry had run out of fuel in the high seas of the Florida Straits, and officers on the two Cuban Coast Guard patrol boats that chased them there tried to persuade the hijackers to return to the island.
The hijackers allegedly threatened to throw passengers from the boxy, flat-bottomed boat into the pitched waves but after much negotiation agreed to let the ferry be towed the 30 miles back to Cuba's Mariel port for refueling.
After the boat was docked in Mariel, west of Havana, Cuban authorities last week eventually gained control of the ferry. Suspects were arrested after a quick-thinking French woman hostage jumped into the water to confuse her captors.
The standoff ended with all the hostages, then the suspects, jumping into the water.
The ferry, the Baragua, was commandeered by hijackers a day after a Cuban passenger plane was hijacked to Key West, Florida, by a man who allegedly threatened to blow up the aircraft with two grenades. The grenades turned out to be fake.
Ten of the Cubans aboard that flight opted to remain in the United States and 19 others asked to go home.
Another Cuban plane was hijacked to Key West less than two weeks earlier.
The hijackings coincided with a crackdown on dissidents in Cuba and rising tensions with the United States.