The British royal met patients undergoing rehabilitation for neurological and orthopaedic problems, and while at the hospital Harry watched patients play wheelchair basketball.
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He also sat in on a swimming lesson and later was invited to join in with a canoe event.
The 29-year-old Prince wore a casual outfit with no tie or jacket, reportedly due to the humid conditions in the country.
The visit, which is designed to enhance the partnership between the UK and the two countries, will see Harry tour hospitals, charities and environmental projects as well as seeing two World Cup matches.
On Monday evening, Harry will attend the Cameroon v Brazil World Cup match, and on Tuesday the Prince will go to the training base used by Team GB and Paralympics GB for the Rio 2016 Olympics followed by the Costa Rica v England World Cup match.
Later in the week the flame-haired royal will visit an environmental project which aims to help protect the Atlantic Rainforest, a social project to help reduce crime and drug abuse, before flying to Chile where he will also meet with an NGO which provides emergency housing for those living in poverty.
DETAILS OF PRINCE HARRY'S BRAZIL AND CHILE TOUR
Although this will be Harry's first time in Chile, he is a familiar face in Brazil after his trip to the country in March 2012 for the Queen's Diamond Jubilee. British sources confirmed that he is the best-known and most popular UK royal in Brazil and will hope to build on the links he forged there during his last official visit.