The Supreme Court said it had agreed to allow Massimiliano Latorre to spend four months at home after the Italian ambassador undertook to ensure that he returned to India to stand trial.
Latorre wants to return to Italy to recuperate after he was hospitalized in New Delhi with cerebral ischaemia - a restricted blood supply that can lead to a stroke.
His lawyers argued that he should be allowed to return to Italy in order to reduce the risk of a stress-induced repeat incident while he awaits the resolution of a case that has caused a diplomatic rift between the two countries.
"In the face of no objection from [the government] of India, we let the marine travel to Italy," said Chief Justice Rajendra Mal Lodha.
Latorre and fellow marine Salvatore Girone are accused of shooting the fishermen while serving as part of an anti-piracy mission on an Italian-flagged oil tanker, the Enrica Lexie, off the southern Indian state of Kerala in February 2012.
The Italian sailors say they mistook the fishing boat for a pirate vessel and fired what were intended to be warning shots.
They have been living at Italy's embassy pending a possible trial and were not allowed to leave India.
The 47-year-old was discharged from hospital on Sunday and is not thought to be in any immediate danger, but Italy's Foreign Minister Federica Mogherini insisted at the weekend that his chances of a full recovery would be increased by being allowed home.
Italy says the pair should be tried on home soil since the shootings involved an Italian-flagged vessel in what Rome insists were international waters. India, however, asserts the killings took place in waters under its jurisdiction.
Court ruling 'encouraging'
Italy welcomed the court's decision, although politicians of all stripes continued to insist Latorre and Girone's detention in India was unwarranted, if not illegal.
In a tweet, Prime Minister Matteo Renzi praised new Indian Prime Minister Narendra Modi and his government, who had decided not to oppose the move.
"Cooperation with the Indian judiciary and credit to Premier Modi and his government. We are working together on so many fronts," Renzi tweeted.
3. Collaborazione con la Giustizia indiana e stima per il premier Modi e il suo Governo. Lavoreremo insieme su tanti fronti.— Matteo Renzi (@matteorenzi) September 12, 2014
That brought an instant rebuke from one of the many critics who have repeatedly attacked the government for not getting both sailors out of India.
"Renzi credits India because they are sending Latorre home for four months after an ischaemia and two years of illegal detention. Are you nuts?" tweeted Giorgia Meloni, leader of the right-wing FDI party.
Defence Minister Roberta Pinotti said in a statement that Friday's decision was "encouraging" but would not reduce Italy's determination to secure a definitive resolution of the disagreement over where the sailors should face trial.
Criminal proceedings against the pair were suspended in March when judges agreed to consider a challenge to prosecutors' jurisdiction in the case and a request for the marines to be allowed home pending its outcome.
The marines were granted a home visit to vote in national elections last year, but India was furious when the Italian government initially said it would not send the men back.
A subsequent U-turn, which followed intense Indian diplomatic pressure, triggered the resignation of Italy's then foreign minister.
Earlier this year, Italy sought help from the US in resolving the long-delayed case soon after recalling its ambassador from India amid worsening ties.