The 1984 Nobel Peace Prize laureate who won the award for his role against the racist apartheid system and worked for healing, arrived in a wheelchair with his wife, Nomalizo Leah Tutu.
Also, among the family members at the service were two of the couple's daughters, Rev. Mpho Andrea Tutu van Furth and Naomi Nontombi Tutu, the Daily Maverick reported.
It was an intimate midday service, with limited attendance due to COVID-19 regulations in South Africa and began with Happy Birthday sung by the assembly.
Tutu was frail and unable to stand up from his wheelchair, but he applauded reverently in the front row, South Africa's Daily Maverick Newspaper reported.
'Always given us hope'
One of Tutu's fellow anti-apartheid activists. Rev. Allan Boesak, who was once president of the former World Alliance of Reformed Churches, led the service for his "friend and brother," saying that the archbishop, despite "seeing it all... has always given us hope."
"Your leadership of the South African Council of Churches was a wake-up call to the church, as it was an alarm bell ringing for the apartheid regime.
"After the vicious repressions of the 1960s, after the Sharpeville massacre, they thought they had silenced the church, but God had other plans, and you came, and you woke up the church, you shook the church up," said Boesak.
From 1978 to 1985, Tutu was general secretary of the South African Council of Churches, which was at the forefront of the struggle against apartheid and was a thorn in the authorities' side.
Tutu was also co-chair of South Africa's Truth and Reconciliation Commission set up by the democratically elected government in 1995 to help heal and reconcile the country after the end of apartheid and is seen as Nelson Mandela as a critical person is shaping the new South Africa.
The former general secretary of the World Council of Churches (WCC) and now presiding bishop of the church of Norway, Rev. Dr Olav Fykse Tveit, wrote about Tutu on this Facebook page. "A life in ministry for justice, reconciliation, unity through a pastoral leadership in prayer, dialogue and prophetic witness. He is a great man. I was honoured to meet him at my visit to South Africa in 2016," said Tveit.
Message from Sweden
Rev. Dr Antje Jackelén, archbishop of Uppsala, also sent Tutu a birthday message on behalf of the Church of Sweden.
"Courage, comfort, transformation, justice and forgiveness are some of the nourishing fruits that have grown out of your service to our common humanity. Those in power were confronted with their accountability and responsibility. Those deprived of their voices were empowered and listened to," said Jackelén.
After the service, Tutu's daughter Mpho said she was "incredibly grateful" to spend the day with her father on his 90th birthday.
"We're so incredibly grateful for the love and the prayerful support that my father has had for his life, his work, his ministry. He couldn't have done all he had without the love, support, and prayers of so many people," she said.