She had her licence to officiate as a priest rescinded in South Africa when she revealed her sexuality and married Marceline van Furth, a Dutch academic, in 2015.
When the Kenyon family discovered Tutu van Furth had been barred, they moved the service from St Michael and All Angels in Wentnor, just south of Shrewsbury near the England-Wales border.
The funeral was moved to a marquee in a neighbouring vicarage so the goddaughter could officiate.
Tutu van Furth told the BBC: "It's incredibly sad. It feels like a bureaucratic response with maybe a lack of compassion.
"It seemed really churlish and hurtful. But as sad as that was, there was the joy of having a celebration of a person who could throw open the door to people who are sometimes excluded."
Desmond Tutu, who died in December 2021, won the Nobel Peace Prize in the 1980s for his work tackling apartheid in South Africa.
He also championed gay rights and campaigned for same-sex marriage.
In 2013, he said: "I would refuse to go to a homophobic heaven. No, I would say sorry, I mean I would much rather go to the other place.
"I would not worship a God who is homophobic and that is how deeply I feel about this ... I am as passionate about this campaign as I ever was about apartheid. For me, it is at the same level."