"The infection was a consequence of treatment for prostate cancer that the Archbishop has received over the past 18 years," a statement said, adding he would continue his recovery at home.
His daughter Mpho Tutu said the cancer was "well under control".
The 83-year-old Nobel peace laureate was last month admitted to a Cape Town hospital, where he underwent a "small investigative procedure" to assess the infection that had afflicted him for several weeks.
The much-loved cleric, who is seen as South Africa's moral leader, was visited in hospital by former president Thabo Mbeki, among other prominent public figures, according to the Desmond & Leah Tutu Legacy Foundation.
Tutu shot to worldwide fame during the apartheid era, leading demonstrations against white supremacist rule while wearing a purple cassock.
He received the Nobel Peace Prize in 1984.
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