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The private service was held at St John's Anglican Church in Johnsonville -- the same church where Mr Ayley regularly played drums.
The church was packed with friends, family and a rottweiler, one mourner said after the service.
In lieu of flowers, the family asked those who attended to give a gold coin donation to Life Flight Trust
"He gave to this charity despite having no money as they braved their way passed (sic) his Rottweilers to ask for a donation some years ago," the order of service said.
"He gave regularly ever since."
The family also thanked their friends for their "phenomenal support" since the crash.
The 29-year-old Otaki man was travelling home on the ill-fated MH17 in which 298 people died when it was shot down on July 17.
Mr Ayley had been on a month-long trip to Europe looking at kennels with plans to import rottweilers.
Earlier today the family said the service would be a chance to gather with friends and family to celebrate Rob's life.
"The service will be held at the church where we have worshipped as a family for 17 years," the statement said.
"Rob played drums there on a Sunday over time with bright blue hair, dreds, a cheeky smile and at times a teenage attitude.
He thought nothing of dropping his drum sticks at quiet poignant moments in the services but brought a new energy to the worship."
The statement went on to say that Rob was a vibrant young man who "had a great sense of family...so it was a great joy to him that he fathered 2 beautiful boys who are so like him in many ways but also have a lovely balance with their Mum's genes as well!".
"Rob lives on in his family, in his boys and in the many memories we all have of him.
"He wasn't a saint, he was no-one important."
Mr Ayley's family said his death was no more tragic than that of anyone who died.
"Death is always a separation from the ones we love and sadness always follows.
"The circumstances of Rob's death are unique as Rob was unique but beneath it all he was a happy man who loved life and did what he could to make others happy too."
The family asked for people to remember Mr Ayley as an "ordinary chap who ultimately achieved some amazing things which shows we should never assume someone's abilities but let them dream dreams and some may come true".
A trust fund has been set up at Westpac Bank, with donations going to the future of Rob's two little boys.