Jones, of Colwyn Bay, Conwy, announced last month that he has a severe type of dementia.
Fellow Python star Michael Palin paid tribute to his "most wonderful friend" before presenting him with the award.
Jones told the crowd to "quieten down" before his son told the crowd it was a "great honour".
Accepting the accolade on his father's behalf, a tearful Bill Jones told the audience in Cardiff: "It's a great honour for dad. We're so proud of him... with the struggles we're having at the moment, it's been hard."
Earlier in the evening, Hollywood actor Leonardo DiCaprio paid tribute in a video message to Oscar-nominated make-up artist Sian Grigg, who won the Sian Phillips award.
It is given to someone who has made a significant contribution to international feature films or network television.
Mali Harries took the best actress prize for her performance as Det Insp Mared Rhys in detective series Hinterland/YGwyll, which also won best television drama.
Mark Lewis Jones won the best actor award for the film Yr Ymadawiad, which tells story of two young lovers who are saved by a man after crashing their car into a ravine in the remote mountains of Wales.
Hinterland/Y Gwyll producer-writer Ed Talfan also won the writer award for the film.
Mr Calzaghe, a documentary film about the career of Welsh boxer Joe Calzaghe, won three awards, including special achievement in a feature/television film and best factual director for Vaughan Sivell.
Will Millard, won the presenters award for Hunters of the South Seas, which explores the lives of people of the Coral Triangle in the Western Pacific, while Newyddion 9, a BBC Wales production for S4C, won best news coverage for its programme Argyfwng y Mudwyr about the European migrant crisis.
Music for Misfits: The Story of Indie, which documents the development of British indie music, won the factual series prize.
The award for live outside broadcast went to S4C's Cor Cymru - Y Rownd Derfynol - coverage of the Welsh choir final.
Those attending the event, which honours the achievements of Welsh television and film makers, included Gotham star Erin Richards, Torchwood and Victoria actress Eve Miles and comedian Elis James.

Christopher Huxtable, 34, from Swansea, had been missing since the collapse in February.
His body was found on Wednesday and workers who carried out the search formed a guard of honour as it was driven from the site in the early hours of the morning.
Ken Cresswell, 57, and John Shaw, 61, both from Rotherham, remain missing.
The body of a fourth man, Michael Collings, 53, from Brotton, Teesside, was previously recovered from the site.
Swansea East MP Carolyn Harris, who has been involved with the family since the incident, said they still did not know all the facts about the collapse.
She said: "I feel very sad. My heart and my prayers go out to the family who have waited desperately for Christopher's body to be found. They can finally have closure, and say goodbye to him and grieve his loss.
"But let's not forget that there's two other families who are still waiting for their loved ones to be returned."
The building was due for demolition when it partially collapsed in February.
Monty Python's Terry Jones has received a standing ovation at the Bafta Cymru awards for his outstanding contribution to television and film.
[NEXT_CONCEPT]
A body found in the ruins of a collapsed building at Didcot Power Station has been identified.