The Prince began a four-day tour of South Africa by sitting down to informal talks over tea with the Noble Peace prize winner and his wife in Cape Town.
Last week the Prince was in Lesotho opening his Sentebale charity's landmark £2 million children's centre for vulnerable youngsters.
The archbishop emeritus told the prince: "I am very touched by your commitment to Lesotho. I taught at the university there and became Bishop of Lesotho.
"It has always had a very soft spot in our hearts, just wonderful that you and the English are helping, thank you very much."
Prince Harry recognised Mr Tutu's lifetime commitment to peace and presented the retired archbishop with the Order of the Companion of Honour, an award given to leading individuals for outstanding achievements in arts, culture and religion.
The 83-year-old has been in and out of hospital on recent months suffering from infections related to prostate cancer.
Mr Tutu, often described as South Africa's moral conscience, particularly since the death of Nelson Mandela in 2013, said about the award: "We are deeply touched".
He added: "We depend so much on other people. I have stuck out in a crowd because you are being carried on the shoulders of others. If the people had repudiated me, where would I be?
"The fact of the matter is that they came along and agreed with me when I said we wanted sanctions against the apartheid regime.
"Despite all of the efforts of the apartheid regime to alienate us, they stood by us and said 'you are our leader'. Without them we I would be nothing. It's as much their award as it is mine."
Mr Tutu also holds the US Presidential Medal of Freedom, and is a Grand Officer of the French Legion d'honneur, he also holds the German Order of Merit Grand Cross, the Gandhi Peace Price and the Sydney Peace Prize.
He was an anti-apartheid campaigner who rose to prominence in the 1980s, when Mr Mandela was still behind bars.
