Bob Dowler said Amanda, known as Milly, touched the lives of everyone she came into contact with.
He praised her independent character and her sense of humour which was often used at his expense.
Mr Dowler also gave details of Milly's Fund, a charity set up to promote personal safety.
He told the congregation of more than 1,000 people: "We will miss Milly's sense of humour.
"Sally (her mother) in particular will miss Milly referring to her as a 'lovely mummy'.
"I will miss asking Amanda where my missing CDs were, as she often borrowed my 1960s CDs.
"Sally will miss her untidy bedroom which was definitely an award winner."
Friend's tribute
Mr Dowler called on local businesses to help with Milly's Fund which he hoped would help prevent other families go through the "pain" the family has faced.
The Dowlers are working with the Suzy Lamplugh Trust which is named after the estate agent who disappeared after meeting a client in 1986.
Earlier, family friend Lindsay Dobson had broken down as she paid her tribute.
She said: "Milly would have made a real mark on this world - a real impact."
Milly's best friend, Hannah MacDonald, read a poem about their friendship to the congregation.
In it, she said that in her dreams Milly is still with her.
She also said that the "living hell" which she was going through along with Milly's family would not ruin them.
Milly's song
A saxophone group from Heathside School, of which Milly was a member, performed two numbers during the service.
One of them, the theme from the film The Spy Who Loved Me, was the last solo Milly ever played on the instrument, during a practice on the Sunday before she went missing.
Pupils at the school were given the day off to attend.
After the service, Milly's sister Gemma released a number of multi-coloured balloons into the sky above Guildford Cathedral.
Police officers investigating the 13-year-old's murder also attended the service.
A private funeral will be held after Milly's remains have been released by the police.