Patel's body was carried by a large group of men into the funeral grounds and through the crowd of mourners as they all prepared to take part in prayers.
An Imam speaking over a loudspeaker system talked about how it is important to pray and respect one another.
He said Patel's love was evident in the large crowd gathered.
As part of his speech, he emphasised the need to forgive those for their sins.
He also thanked the police, Prime Minister Jacinda Arden and everyone who has helped in the past week since the attack.
"I would like to thank them all from the bottom of my heart," he said.
The cemetery fell silent before the mourners recited the Salat al-Janazah, Islamic funeral prayer and he was buried.
Speaking after the funeral for Imam Hafiz Musa Patel, Vice President of the South Auckland Muslim Association, Abdul Shakeel Ahmed, said Imam Patel was "one of the greatest men we have seen in Fiji".
"He was born in India and came to Fiji more than 25 years ago. He served the community Muslim community in the whole of Fiji as well as New Zealand and Australia," he said.
"He has been all the time a powerful man and preaching to everybody the facts and figures to be a powerful and good Muslim."
Ahmed said the thousands of people who turned out to the funeral showed how patient and giving Imam Patel was.
"I met Patel so many times when I was back in Fiji 20 years back when I was a student and went to his mosque - and he was a very nice guy," he said.
Ahmed said Imam Patel's two sons and his wife attended the funeral.
"It is very sad for our community. I wish the family all the best for a happy life in Australia," he said.