Pele had the surgery at the Israelite Albert Einstein hospital.
"The procedure was a success and the patient is back in his room," a brief statement from doctors said.
Considered by many the game's finest player and the only man to have won three World Cups, Pele had also been admitted to hospital in France last week after suffering a fever following an event in the city with French World Cup-winner Kylian Mbappe.
He was soon released but his doctors in Brazil decided to admit him again when he returned home on Tuesday.
The 78-year-old former Santos and New York Cosmos player has suffered from kidney and prostate problems and also had hip replacement surgery in recent years.
(Reporting by Andrew Downie, editing by Pritha Sarkar)
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