"He left this morning at 10:30am, not wanting to depart from the side where the press were waiting," said a spokesman for the clinic in the centre of Ibiza.
A spokesman for the former player confirmed his departure in an email message.
Ronaldo said Sunday he was being treated for a severe bout of flu infection after being taken to hospital Friday.
Local newspaper Diario de Ibiza said the former Real Madrid star had been treated in intensive care for pneumonia at the city's public hospital before being transferred to the clinic.
The 41-year-old, who was named FIFA's world player of the year three times prior to his retirement from football in 2011, is a regular visitor to Ibiza, where he owns a house.
He won his first cap for Brazil as a 17-year-old and went on to score 62 goals in 97 international appearances, including both goals when Brazil beat Germany 2-0 in the 2002 World Cup final.