Friends and band members carried the coffin
Lee, who was 33, was found dead at his Miami home on 7 January after committing suicide.
Bandmates Grant Nicholas and Taka Hirose carried Lee's metallic blue coffin into the church with his brother Andrew and some of his friends.
Lead singer Nicholas paid tribute to his friend, who he met on the local band scene in south Wales 16 years ago.
"I hope you are at peace now. Forever young. Love always," he said.
Fans of the hit band had been told access to the service at St Mary's Roman Catholic Church would be "unrestricted".
Mourners included drummer Stuart Cable from fellow Welsh band Stereophonics.
But Lee's widow Tatiana and two-year-old son Cameron did not attend after holding a private service in Miami.
A floral tribute spelling the name Feeder was alongside the coffin, as were flowers in the shape of a drum from his parents Pat and Norman.
During the service, the group's manager Matt Page said Lee would always have a place in the band.
"We know that time will very slowly heal. We are determined to continue. We still have a long way to go," he said.
"Jon Lee will always be a person in this band. His character and ethos will be there."
Father Brian Cuddihy said he had not heard of Feeder before last week, but had been on a "swift learning curve" since then.
A photograph of Jon playing at the Glastonbury Festival he had seen showed the drummer "filled with music, filled with happiness", he said.
"In that I saw the real Jon," he said.
After the service, Lee was buried at St Woolas Cemetery.
'Suffering'
The drummer's family have asked that instead of sending flowers, fans could donate money to a charity, the Noah's Ark Appeal, which is raising funds to build the first children's hospital in Wales.
In a letter to fans earlier in the week, Tania Lee said: "My children and I have had our services in Miami for our Jon and therefore will not be at his service this coming Friday in Wales.
"We are all suffering very much and cannot bear any more. Our hearts will be there with him, his family and friends."
Lee was a founding member of Feeder, who had four UK top 20 singles, including Buck Rogers and Just A Day.
The band's official website is creating a virtual scrapbook of fans' memories of Jon Lee which will be presented to his family.