Hopes of finding survivors were revived when the navy said Saturday that its bases had received seven satellite calls attributed to the submersible.
The submarine had reported a malfunction, had surfaced, and was headed back to its base when the Navy lost contact with it.
The noise was heard in the South Atlantic about 220 miles from the Argentine coast and at a depth of about 650 feet.
Hopes of discovering the ARA San Juan received a setback on Monday when the navy confirmed that failed satellite calls traced to the area on Saturday did not come from the submarine.
The vessel was returning to the Mar del Plata Naval Base south of Buenos Aires at the conclusion of a routine patrol to the far southern port of Ushuaia.
The Argentinian navy is focusing its search in an area of 35 square nautical miles about 330 miles from the coast of Argentina.
"I also pray for the men of the crew of the Argentine military submarine which is missing", the pontiff said.
"Do not have any doubts, this is what we say to family members these days, we continue to redouble our efforts tomorrow, afternoon and night looking for air, sea and the bottom of the sea until the ship appears".More news: 6th Miss World win draws India level with Venezuela
The first rescue system - the submarine rescue chamber and an underwater, remotely operated vehicle - was flown from Miramar to Comodoro Rivadavia, Argentina, where it's expected to arrive Sunday. The Argentine sub has been missing in the Argentine Sea, and the subsequent search is entering its fifth day.
Crew members' relatives gathered at the Mar del Plata naval base, waiting for news.
More than a dozen boats and aircraft from Argentina, the United States, Britain, Chile and Brazil have joined the search effort. The submarine also has an emergency position-indicating radio beacon (EPIRB) and a satellite communications buoy that can be deployed if the vessel is in distress.
Two U.S. aircraft carriers were part of the search team.
"Yesterday's news was something of a respite for us, to know that there is life", Claudio Rodriguez, the brother of a crew member, said on television channel A24 on Sunday morning.
The Argentine military has also been working with a USA company that specializes in satellite communication to determine the location of the submarine.
The U.S. Navy said the Bluefin 12D diver can rescue six people at a time, if the Argentine submarine is found. Officials said if the craft was intact but sunk, crew would have a week to 10 days of oxygen, but much depends on other circumstances, according to CNN.