The two men, Celso Roberto Scafi and Claudio Rogerio Carneiro Fernandes, are both urologists who practiced medicine in the southeastern state of Minas Gerais.
But officials allege they also were part of an organ-trafficking "mafia" in which kidneys, livers and other organs and body tissues were illegally removed from patients, some of whom were still alive, and sold.
The men were convicted at a trial in February 2013 but appealed to a higher court, which on Thursday upheld the lower court's verdict.
A judge in the case last week sentenced the men to prison terms of 17 and 18 years, according to news reports. Their licenses to practice medicine also have been revoked.
Authorities said a search was underway for a third physician in the scheme, anesthesiologist Sergio Poli Gaspar, who failed to turn himself in to authorities and is considered a fugitive from justice.
The case dealt with a 10-year old boy, Paulo Veronesi Pavesi, whose organs were removed without permission and sent to the United States after his accidental death in a fall.