The four-month-old royal made his first appearance of Harry and Meghan's Africa tour by posing with one of the heroes of the anti-Apartheid movement as he was held by his proud parents.
Archie was the centre of attention as the group, which included the archbishop's daughter Thandeka Tutu-Gxashe.
The archbishop's daughter also joked about his comfort in front of the camera, saying: "You like the ladies. He's going to be a ladies man."
The veteran Nobel Peace Prize winner, who was effectively the leader of the liberation struggle during Nelson Mandela's long imprisonment, said he was "thrilled by the "rare privilege and honour" to meet the royals.
The 87-year-old cleric spent half an hour with the couple and Archie at the historic premises of his Legacy Foundation in Cape Town, the Old Granary, a restored centuries old edifice built by slaves.
For the informal meeting Meghan sat with Archie on her lap and Harry beside her, while the retired archbishop and his daughter sat opposite them.
The group laughed as they watched the duchess take her son's arms and dance with the young royal who appeared to be wearing dungarees, a top and socks.
Footage of Meghan and Harry making their way to see the elderly statesman has been posted on the couple's official Instagram account.
Archie is carried by Meghan and the four-month-old is seen smiling and laughing as the Sussexes walk.
The duchess revealed on Tuesday her "transition" to motherhood was made easier as son Archie has been a "wonderful" baby.
Meghan opened up about life as parent when she and Harry were invited to meet a Muslim Cape Town family, and have afternoon tea in their home.
The duke also talked about being a father and revealed he likes to bond with his four-month-old son by letting him fall asleep on his chest.
When Meghan and Harry first arrived Mr Tutu greeted them with laughter and beside him was his daughter who is chief executive officer of the Desmond Tutu Desk campaign, which creates portable desks for schoolchildren.
The foundation is the global rallying point for the archbishop's values about respect of people and the earth.
Established by the cleric and his wife Leah Tutu, its mission is to pass on the statesman and his partner's wisdom and instil their values in the next generation of leaders.
"We are enormously grateful to welcome the Duke and Duchess to our magnificent space, and for their love and respect for the Arch," said foundation chair Niclas Kjellstrom-Matseke.
Harry last met the archbishop in November 2015 when the Queen named him as an honorary member of The Order of the Companions of Honour, in recognition of his services to UK communities as well as international peace and reconciliation.
His Royal Highness Prince Harry hand-in-hand with Archbishop Desmond Tutu on arrival at the Desmond & Leah Tutu Legacy Foundation today. pic.twitter.com/irsPz6e6Um— TutuLegacy (@TutuLegacy) September 25, 2019
He was also a recipient the 1984 Nobel Peace Prize for his efforts in resolving and ending Apartheid.
Born in 1931 in Klerksdorp, Transvaal, South Africa, he became the first Black Anglican Archbishop of both Cape Town and Johannesburg.
During the 1980s, he played a role in drawing national and international attention to the iniquities of Apartheid.
In 1993, South African Apartheid finally came to an end, and in 1994, South Africans elected Mr Mandela as their first black president.
Mr Mandela also appointed Tutu to head the Truth and Reconciliation Commission, tasked with investigating and reporting on the atrocities committed by both sides in the struggle over Apartheid.
The father of four chaired the commission and since then has continued to draw attention to a number of social justice issues.
Although he officially retired from public life in the late 1990s, the archbishop continues to advocate for social justice and equality across the globe.
After the meeting Harry left to prepare for a solo visit to Botswana, the first of three African countries the duke will visit while his family stay in South Africa.
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