Named after the Araguaia river where it was found, the species is only the fifth known of its kind in the world.
Writing in the journal Plos One, the researchers say it separated from other South American river species more than two million years ago.
There are believed to be about 1,000 of the creatures living in the Araguaia river basin.
River dolphins are among the world's rarest creatures.
According to the IUCN, there are only four known species, and three of them are on the Red List, meaning they are critically endangered. These dolphins are only distantly related to their seafaring cousins, tending to have long beaks which let them hunt for fish in the mud at the bottom of rivers.
One of the best known species, the Yangtze river dolphin or baiji is believed to have gone extinct in about 2006.
South America though is home to the Amazon river dolphin, also known as the pink dolphin or boto, said to be the most intelligent of all the river species. The new discovery is said to be related to the Amazonian, although scientists believe the species separated more than two million years ago. "It is very similar to the other ones," said lead author Dr Tomas Hrbek, from the Federal University of Amazonas.