The discovery of Inia araguaiaensis in the waters of the Araguaia River was published in a study posted online in the scientific journal PLoS ONE.
The new species is the third ever found in the Amazon region, lead author Tomas Hrbek, a biologist at the Federal University of Amazonas in the city of Manaus, said.
"It was an unexpected discovery that shows just how incipient our knowledge is of the region's biodiversity," Hrbek told the British newspaper the Guardian.
"River dolphins are among the rarest and most endangered of all vertebrates, so discovering a new species is something that is very rare and exciting," he said.
Analysis and comparison of DNA samples of several types of dolphins from the Amazon and Araguaia river basins led to the conclusion the Araguaia dolphins are a separate species, Hrbek said.
"The Araguaia dolphin is very similar to its Amazon River cousin although somewhat smaller and with fewer teeth," he said. "People always saw them in the river but no one ever took a closeup look at them."
There is concern for the species' survival, he said, with an estimated 1,000 dolphins living in the 1,630-mile-long river.