He has signed an initial two-year deal with the option of extending his stay at Stade Marcel Michelin for a further 12 months.
"We are delighted to welcome Jonathan next season," said Clermont sporting director Jean-Marc Lhermet
"His profile fits the game we play perfectly and he will bring us a lot.
"Despite his young age, he has a huge experience of top 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 he'll be playing in yellow and blue.
"We're sure that his class and determination will help us win new trophies in the years to come."
The news comes as a major blow to the Scarlets, who currently top Pool Four with Clermont in third place.
They face last season's runners-up in back-to-back matches in December, but will not be able to call upon Davies to face his future team due to injury.
He suffered a pectoral injury during Wales' autumn loss to South Africa on Saturday and could be out of action for up to five months, ruling him out of the remainder of the Heineken Cup group stages.
"Jon has established himself in recent seasons as a world-class centre for Scarlets, Wales and now the British and Irish Lions," said Scarlets head coach Simon Easterby
"He has worked hard throughout his career to date and has now shown his ability on the highest of rugby stages having grown into his role as a senior player here in our region.
"He has gained valuable experience and developed quickly with the Scarlets in recent years as part of a group of young internationals that are from our region and have successfully gone onto achieve honours with Wales.
"He has always taken great pride in having his rugby roots in West Wales and I know this will have been a tough decision for him personally, and probably one of head over heart.
"His commitment to our region during this, the first part of his rugby career has been evident and I know that having grown up in our region he will always want to be closely associated with Scarlets rugby now and in the future.
"He will give his all in his last season with us I am sure and will lead from the front. But for now, our focus is to support Jon as he recovers from his injury and gets back to full fitness as soon as possible."