The service at St Edward's Church in his home town of Stow-on-the-Wold, Gloucestershire was attended by hundreds of mourners, mostly friends and family members.
The 57-year-old star was found dead in a hotel room in Las Vegas on 27 June after suffering a suspected heart attack.
Entwistle enjoyed success for 35 years
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Entwistle's coffin was followed into the church by members of his family, including his girlfriend, Lisa Pritchard-Johnson.
The service was broadcast on loudspeakers to the crowd of well-wishers and fans gathered outside.
It began with words from the Rev Colin Wilson, a family friend.
He said: "I think he would want us all to be strong, determined, unafraid of the future, ready to meet every challenge, to believe in ourselves and in each other."
He said Entwistle was now "reunited with Keith up there making great music".
Floral tributes
Following a reading of a Joyce Grenfell poem, which urged mourners to go on with life, the hymns Jerusalem and The Lord's My Shepherd were sung.
Afterwards, singer Daltrey and guitarist Townshend hugged as they left the service.
The entrance to the church was surrounded by floral tributes including one reading "RIP Ox", referring to the bassist's nickname. In the hearse were tributes shaped like a champagne bottle and a guitar.
Girlfriend Lisa Pritchard-Johnson was among the mourners
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"He had a wonderful sense of humour. He was always ready to help out. He is already being missed by lots of us - it is a hell of a hole to replace," Mr Johnston added.
Entwistle's website said a memorial service would take place in London later in the year, and fans would be invited to attend to celebrate his life.
A small number of fans had gathered outside the church to hear the service.
Sudden death
Alan Markall, 56, from South Norwood, south London, said he had followed The Who since they formed in 1964.
"John was the best bass player in the world. They could have gone on for another 20 years - I hope they will but it will not be the same now."
The musician's sudden death came almost 25 years after The Who's original drummer, Keith Moon, died of an accidental drug overdose.
The Who first formed in London in 1964 and were one of the leading rock bands through the 1960s and 70s scoring hits with Pinball Wizard and My Generation.
Entwistle, born in Chiswick, London, paired up with The Who front man Roger Daltrey in a forerunner to the group in the early 1960s.