The controversial chat show host, whose reported £18 million (€20m) three-year contract was due to expire in the summer, insisted his decision was not related to his pay packet.
His decision comes just more than a year since the notorious Sachsgate scandal, over which Ross was suspended for three months, and followed reports that Ross’s future at the BBC was looking increasingly uncertain.
Cork-born comedian Graham Norton, who has just signed a new deal with the BBC, had been reported to be a rumoured replacement for Ross’s Friday night chat show.
Friday Night with Jonathan Ross, the star’s Saturday morning Radio 2 show and his film review programme have made Ross one of the Corporation’s biggest stars, but his high profile has also landed him in hot water.
Yesterday the broadcaster, 49, said of his departure: “I think it’s probably not a bad time for me to move on and probably not a bad time for them (the BBC) either.”
He said he had made the decision not to re-negotiate his current contract, which expires at the end of June, in the last fortnight.
Ross said he was “grateful to the BBC for such a marvellous experience” and that he would “miss” making all his BBC shows.
He said in a statement: “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.”
Ross had offered to take a 50% pay cut when his contract expired, which would have slashed his annual salary by £3m.
Jana Bennett, director of BBC Vision, said she could “understand” Ross’s decision “following a difficult year”.
She said: “It’s been a difficult year for him and I understand why he feels it’s the right thing to do.”
BBC creative director Alan Yentob said the year “with all that scrutiny and attention... has obviously been a tough one for him” and that he wanted to “go out with a bang”.
Asked about speculation that Norton, said to be receiving £4m (€4.5m) to stay at the Corporation for another two years, was being lined up to replace Ross, he said: “You don’t need to compare Graham with Jonathan Ross. No decisions have been taken with that (Friday night) slot.”
A BBC insider said Ross, who has been one of the biggest broadcasters of his generation, was not pushed.
“This was never about money,” he said. “It was Jonathan Ross coming and saying ‘given everything that’s happened over the last year, I think it’s time to take a break’. We sort of agreed.
“It was never the case of saying ‘we were waiting to push him out of the door and waiting for him to leave’.
“No deal was ever going to be the right deal. It’s been a tough year and it was going to be very difficult moving forward.”
Ross, known for his flamboyant dress sense and inability to pronounce the letter R, could now move to Channel 4, ITV or Sky or move to the US.
Speculation about signing a deal in the US mounted when he Tweeted that he was meeting someone from Los Angeles.
Later 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.”
In a later message to his fans, Ross Tweeted: “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!”
Fans called Ross’s announcement the “end of an era”, saying they were “sad” and “gutted” about the decision, while others pondered how much money it would save the BBC.
Ross has become an increasingly controversial figure in recent years for making inappropriate comments.
In 2008, he was suspended for three months after making a series of phone calls to actor Andrew Sachs on Russell Brand’s Radio 2 show.
Yesterday Ross said he would continue hosting the Bafta Film Awards, Comic Relief and other BBC specials.