It means that seals and sea lions probably contracted the disease from a host animal from Africa, where the disease likely originated, and swam across the Atlantic to South America.
The mammals were probably eaten by coastal people who were themselves then infected and spread the bacteria to others, said the study, published in the journal Nature.
"The source of tuberculosis in the New World has long been a question for researchers," Elizabeth Tran, the NSF's biological anthropology programme director said in a statement.
"This paper provides strong evidence that marine mammals may have been the likely culprits."
The analysis also revealed that tuberculosis in the form we know it was much younger than originally thought, and probably only evolved in Africa about 6,000 years ago.
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.