Wales assistant coach Rob Howley revealed on Tuesday that Davies has secured "full release" as part of his two-year contract at Stade Marcel Michelin.
However, Clermont's announcement they had captured Davies coincided with confirmation from the Wales camp that he requires surgery on the ruptured pectoral muscle he suffered in last Saturday's punishing 24-15 defeat against South Africa.
It means the 37 times-capped Scarlets centre, who started all three British and Irish Lions Tests in Australia earlier this year, faces up to four months' rehabilitation and looks set to miss part, if not all, of Wales' RBS 6 Nations title defence.
And in a second major injury blow, Wales have also lost Lions prop Adam Jones for the remaining autumn appointments with Argentina, Tonga and Australia due to calf muscle trouble.
Davies, 25, will join Wales colleagues Jamie Roberts, Dan Lydiate, James Hook, Luke Charteris and Lee Byrne in France's Top 14 after ending speculation about his future.
"I think it is a blow for Wales," Howley said. "He will be sorely missed.
"What you saw in the summer in terms of his performances for the Lions was exceptional. He has been outstanding on and off the field.
"I am aware he is a very ambitious player. He wants to be part of a winning team, winning medals, and obviously he has gone to a side that he feels is going to be right up there in European rugby.
"He has got full release, similar to Jamie Roberts and Dan Lydiate, so in terms of his availability to play for Wales in an autumn series he would be fully available."
But Howley added: "We want our players in Wales.
"There is the culture, the fantastic training facilities that we have, the facility of working with the physios, along with the regions, and the conditioning staff. When they go to France or England, we lose that.
"It is not out of sight out of mind, but we want our players in Wales because ultimately Welsh supporters want to watch the best and we, as coaches, want to watch the best on a Friday and Saturday, as opposed to going over to France or England."
Davies has the option of a third season with Clermont and their sporting director Jean-March Lhermet said: "We can only be delighted to welcome Jonathan. His profile fits perfectly to the game that we practise.
"Despite his young age, he has a huge experience of high-level matches and is one of the world's best players in his position. He will be an asset to our team.
"Jonathan decided to leave Wales for a new adventure and we are happy that it is with the 'yellow and blue'.
"In addition to his class, he has determination to help us win new titles in the years to come."
Davies will join a star-studded Clermont squad that contains players such as Aurelien Rougerie, Morgan Parra, Sitiveni Sivivatu and Wesley Fofana, with the brilliant France international Fofana likely to be Davies' midfield partner.
And Davies' departure puts into even sharper focus the futures of several Wales colleagues. Skipper Sam Warburton, full-back Leigh Halfpenny, prop Adam Jones and lock Alun-Wyn Jones are among those attracting considerable interest from abroad.
It is understood that the Welsh Rugby Union has earmarked a £1million fund to help the regions keep their prize assets.
Scarlets chief executive Mark Davies said they had done everything in their power to keep the Wales star at the Llanelli-based region, but wished him the best in his new venture.
"Jon has taken as much time as he could to consider each element of the tremendous opportunities available to him, and he has ultimately now had to make his decision on the best route for him as an individual at this point in his rugby career," Davies said.
"Unfortunately for us that will result in Jon playing in France over the period of his next contract, but we remain immensely proud of everything Jon has achieved with his region and completely respect his decision to extend his horizons and take this significant opportunity at this time."
In a statement, the WRU said: "The WRU emphasises that it always prefers elite Welsh-qualified players to contract to one of the four regions in Wales, but understands the player now feels he requires new playing challenges.
"Davies has explained that he believes the move will aid his development and says he remains totally committed to winning more caps for Wales and also competing for a place in the Rugby World Cup 2015 Welsh squad."
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