Tutu said Mandela had been given "the send-off he deserved" but apologised for the failure to match the icon's renowned openness by not including the country's main white Afrikaans church.
"Madiba would have been appalled, for he was quite determined to be inclusive," said Tutu, referring to Mandela's clan name, in a statement late yesterday.
While the funeral itself was "superb", Tutu also challenged the leading role of ruling African National Congress (ANC) officials at the main events.
Known for his no-holds barred frankness, Tutu has been openly critical of the South African government.
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At the last minute, he reversed a decision not to attend Sunday's burial after saying he was not going because he had not been invited.
Tutu singled out the failure by faith leaders to include a representative from the white Dutch Reformed Church -- which supported the apartheid system -- at Mandela's official memorial and state funeral.
"The most blatant exclusion was of the Afrikaner community," said Tutu, who hosted Mandela on his first night after his release after 27 years in apartheid prison.
Mandela had reached out to the Afrikaans community, he said, whether lunching or having tea with widows of apartheid presidents or donning a Springbok rugby jersey.
An Afrikaans verse of the former apartheid national anthem was also retained in its multi-lingual successor adopted after the 1994 all-race elections.
"To the extent that I can do so meaningfully, I apologise to our sisters and brothers in the Afrikaner community," Tutu said.