The study offers answers to a number of long-standing questions about TB in the ancient Americas.
Genetically, modern strains of New World TB are closely related to European ones, which led to the conclusion that Europeans introduced the disease after Genoese navigator Columbus's first contact with Amerindians in 1492.
Yet there is archaeological evidence in skeletons and mummies of tuberculosis in the Americas hundreds of years earlier.
Some have suggested the disease must have spread with early humans out of Africa, before the Bering land bridge between Siberia and Alaska was flooded at the end of the last ice age about 11,700 years ago.
But this fails to explain the European genetic likeness, or the fact that TB is probably a younger disease than that.
The latest study concluded that TB bacteria in the three ancient skeletons were different to strains found in humans in the Americas today.
Having been initially brought over by sea mammals, the disease seems to have been replaced by European strains.
"The connection with seals and sea lions is important to explain how a mammalian-adapted pathogen that evolved in Africa around 6,000 years ago could have reached Peru 5,000 years later," said co-author Johannes Krause, of the University of Tuebingen in Germany.
"A marine introduction seems the most likely way that the disease could have reached humans in the Americas thousands of years after the inundation of the Bering land bridge, when terrestrial movements into the Americas was no longer possible."
More than 8.6 million people fell ill globally with tuberculosis in 2012, according to the World Health Organization, and 1.3 million died from it -- making it the biggest killer disease after HIV.
The strains that still exist in seals and sea lions today can still make people ill, though it happens extremely rarely, the researchers said.