The controversial broadcaster is leaving after 13 years at the Corporation.
Ross has been one of the biggest faces at the BBC, with his Friday night chat show, his Radio 2 show and his film review programme.
His salary, a reported £18 million over three years, and the scandal over actor Andrew Sachs have recently caused controversy.
Ross, 49, said in a statement that he had decided not to renegotiate his contract when it ends at the end of July.
He said: "Although I have had a wonderful time working for the BBC, and am very proud of the shows I have made while there, over the last two weeks I have decided not to re-negotiate when my current contract comes to an end.
"While there I have worked with some of the nicest and most talented people in the industry and had the opportunity to interview some of the biggest stars in the world, and am grateful to the BBC for such a marvellous experience.
"I would like to make it perfectly clear that no negotiations ever took place and that my decision is not financially motivated.
"I signed my current contract with the BBC having turned down more lucrative offers from other channels because it was where I wanted to be and - as I have said before - would happily have stayed there for any fee they cared to offer, but there were other considerations.
"I love making my Friday night talk show, my Saturday morning radio show and the Film Programme, and will miss them all.
"I look forward to continuing work on these shows until the Summer, and I will continue hosting the Bafta Film Awards, Comic Relief and other BBC specials.
"Working at the BBC has been a tremendous privilege, and I would like to thank everyone who has watched and listened so loyally over the last 13 years."
A spokeswoman for Sachs said the actor was busy working and unavailable for comment.
The news follows reports that Ross's future at the BBC was looking increasingly uncertain.
Graham Norton, who is seen as a chat-show rival, was a rumoured replacement for his Friday night chat show, according to reports, while Mark Kermode could have been lined up to take the star's review slot, Film 2010.
If that happened, Ross would have been left with his Saturday morning Radio 2 show and a huge pay cut.
Ross had offered to take a 50 per cent pay cut when his contract expired, which would have slashed his annual salary by £3 million.
But his spokesman said he was not in the middle of pay negotiations and said he would continue at the BBC until the summer.
Yesterday, Ross wrote on his Twitter page that he was meeting someone from Los Angeles. The Tweet followed speculation that the star would go to work in the US.
He wrote: "It's annoying but someone has flown in from LA so it would be rude not to show up!"
Today he Tweeted: "Good morning. My day is turning out to be far more interesting then I had anticipated! See you later - have a good one."
Jana Bennett, director of BBC Vision, said she could "understand" Ross's decision "following a difficult year".
She said: "Jonathan Ross has told us that he's decided not to pursue the renewal of his contract with the BBC.
"Jonathan is an extremely talented broadcaster and his programmes for BBC TV and radio have been a great success.
"However, it's been a difficult year for him and I understand why he feels it's the right thing to do.
"I'm pleased that Jonathan will continue to apply his considerable abilities to the remaining six months of Friday Night, Film 2010 and his Radio 2 show, and I'm delighted that he will continue to present the Bafta awards and Comic Relief for BBC Television."
Ross has been one of the biggest broadcasters of his generation.
In 2008, the controversial host was suspended for three months making a series of phone calls to actor Andrew Sachs on Russell Brand's Radio 2 show.
Ross and Brand's messages sparked more than 50,000 complaints - and led to Brand's decision to quit his radio show.
Mark Linsey, controller of entertainment commissioning at the BBC, said conversations had been taking place over the past few weeks.
He said: "It's something that has been finalised over the last few days."
He said Ross had gone on record as saying the situation was not about money.
"He likes and enjoys working with the BBC," Mr Linsey said.
"This is a decision he has made himself."
He said Ross "remains a very talented broadcaster".
He added that the star was having some time out and spending time with his family.
Mr Linsey was speaking at a BBC 3 launch in central London.
In a later message to his fans on Twitter, Ross said: "Hello again. Thanks for all the kind words about my decision.
"I feel sad that I can't keep making the shows so many of you love!"
He added: "Don't worry, I won't stop tweeting!."
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