The two Italians-- Massimiliano Latorre and Salvatore Girone left by AI's Kochi-Delhi flight at 8 pm, airport sources said.
They were accompanied by Italian Consul General in India Giampaolo Cutillo and other officials.
The apex court had in its order stated that the two would be shifted to Delhi from Kerala and be under the 'custody' of the Supreme Court till the Centre constitutes a special court to hold their trial.
Earlier, the Kerala High Court has permitted two-weeks Christmas reprieve to the marines, who had returned to the state on January 4.
The marines were arrested on February 19 last year after they allegedly shot dead two Indian fishermen-- Jelestine and Ajesh Binki off Alappuzha coast on February 15 from the merchant vessel 'Enrica Lexie' suspecting them to be Somali pirates.
The two are presently out on bail and were staying in a hotel here.