The pre-dawn incident on Thursday unfolded when the two fugitives commandeered a bus carrying several passengers to get to an aircraft on the tarmac of terminal two, which services charter flights between Havana and the US.
The bus passengers were left unharmed.
A third deserter was captured earlier but the ministry did not specify when.
Cuba blamed the attempted hijack on the US policy of encouraging Cubans to escape to the US by offering them virtual automatic residency.
“The responsibility for these new murders falls on the highest US authorities, adding to a long list of terrorist acts that Cuba has been victim of for almost half a century,” the government said.
In March 2003, two domestic passenger jets were hijacked to Key West, Florida.
A month later, three men who hijacked a Havana Bay ferry in a bid to cross the Florida Straits were executed by firing squad.