He leaves Welsh rivals Newport Gwent Dragons at the end of this campaign and will join his Parc y Scarlets colleagues for pre-season training in July.
The 19st 11lb 26-year-old tight-head has played 119 games for the Dragons since his debut around six years ago, and seven times for his country.
Scarlets head coach Nigel Davies said: "We're delighted to have signed Rhys. He will add strength and skill to our pack as we prepare for a big season ahead.
"Importantly, he adds to our pool of Welsh talent and I know that his workrate and power will make him a favourite with Scarlets supporters.
"He's determined to progress as a Heineken Cup and international player so I think we can expect big things of him in 2009-10 and beyond.
"We're firming up the look of the squad for next season with plenty for supporters to look forward to. Our future is all about responsible decisions on the playing side and cementing a balanced squad that can perform well in Europe. To do that, we've made it a priority to strengthen key areas of our group with quality players. Adding Rhys to our line-up, is a good example of that."
Thomas, a member of Warren Gatland's RBS Nations squad, said: "It was a pretty easy decision to join the Scarlets; they're a region with a strong tradition of being successful and they have a group of talented players and coaches. I'm friendly with a good few of the players having been in the Wales squad with them - we get along well.
"A major factor in my decision was Parc y Scarlets; it's a great stadium with superb training facilities on site. The indoor training centre on site is amazing.
"I've worked with Nigel Davies before, when he was part of the Wales set-up, and I'm greatly looking forward to working with him again on a daily basis.
"It's my aim to help get the Scarlets back into the later stages of the Heineken Cup and perhaps, to winning the Magners League. I think that being at the Scarlets will also help me push ahead with my international ambitions.
"Newport RFC, the Newport Gwent Dragons and the Rodney Parade crowds have been good to me; they've been a huge part of my life for eight years and I've had a great time there. I've played a lot of games there and have made a lot of friends. I wish them all the best for the future."
Feted for his dynamic play in the loose, Thomas has carved out the reputation as an athletic player who usefully pops up in areas you wouldn't normally expect to see a front row member.
Born in Johannesburg, Thomas attended school in the city and went on to represent the South Africa Academy and the Pirates club. However, he entered mainstream rugby in Newport, Gwent, the home town of his father Colin, an engineer who had gone to work in Africa.
Joining Newport RFC as an 18-year-old, Thomas progressed through the ranks and made his debut for the Black and Ambers senior XV in 2003, soon rewarded with a Dragons development contract. He made 22 appearances for Newport RFC between 2003 and 2004, scoring four tries.
In October 2003 he scored a try on his debut for the Dragons, as a replacement against the Glasgow Warriors. In 2003-04 he played 16 games for the Dragons, almost doubling this the following season and scoring two tries as the team finished fourth in the Celtic League.
Thomas, who has represented Wales at U19 and U21 levels, was part of the youthful Wales senior squad that toured Argentina in the summer of 2006. He gained his debut full cap on the tour, coming on as a second half replacement for Adam Jones.
The 2006-07 season saw Thomas out of action for six months but he still received a call-up to the Wales squad ahead of the November 2007 squad to face South Africa in the initial Prince William Cup match at the Millennium Stadium; he made the starting XV.
January 2008 saw Thomas receive a call-up to Gatland's RBS Six Nations squad; the prop started in the victory over Italy at the Millennium Stadium in the Grand Slam winning campaign and figured against Canada in November last year.
He started in both Dragons games against the Scarlets this season.
The Scarlets face a testing friendly trip to Newport Gwent Dragons this week (Thu, March 26), followed by an April 4 resumption of Magners League action with the visit of Glasgow to Parc y Scarlets.