The Argentine pontiff's prayers come as Argentina's Navy doubled its search for the sailors after picking up seven distress calls.
In a telegram addressed to Bishop Santiago Olivera, the head Military Ordinariate of Argentina, Vatican Secretary of State Cardinal Pietro Parolin noted the Pope's concern for the sailors, Vatican radio reports.
It also expressed the Pope's spiritual closeness to the families of the sailors, and to the military and civil authorities of the nation.
He also noted the Holy Father's encouragement for the efforts being made to find the vessel.
The Navy said on its Twitter account that the brief communication attempts "indicate that the crew is trying to re-establish contact, so we are working to locate the source of the emissions".
However, Argentine authorities have clarified that it has not been confirmed the calls came from the submarine, the ARA San Juan.
Strong winds and twenty-foot waves continue to hinder the operation - with the UK among those helping.
Earlier on Saturday, Navy spokesman Enrique Balbi said the area being searched off the country's southern Atlantic coast has been doubled as concerns about the crew's fate grew.
He said there are a number of reasons to explain the submarine's disappearance, including "a problem with communications" or with its power system.
Meanwhile, relatives of the crew members gathered at the Mar del Plata Naval Base in the hopes of hearing news about their loved ones.
Marcela Moyano, wife of machinist Hernan Rodriguez, told television network TN: "We feel anguish.
"We are reserved but will not lose our hope that they will return."
