The writing was on the wall for the deal to eventuate after Thomas - along with inevitable fellow departure Heath Shaw - was not present for the Magpies' best and fairest night on Friday.
Thomas joins former coach Mick Malthouse and ex-Pies fitness coach David Buttifant at Visy Park, and also close friend and former Collingwood chief executive Greg Swann.
The four-year-deal is believed to be worth $2.5million.
Thomas, who played just five games in 2013 due to a persistent ankle injury, said he was looking forward to a fresh start at the Blues.
"It has been a tough couple of years for me and it felt like the right time to move on," Thomas said.
"I'm grateful Carlton has given me the opportunity.
"I'm excited about joining players like Marc Murphy and Chris Judd, and of course the chance to work with Mick again.
"It will be a new challenge and one I’m looking forward to."
Collingwood president Eddie McGuire lashed out last Friday night, claiming a 'pervasiveness of selfishness' had infiltrated the club - in regards to the impending departures of Thomas and Shaw.
But coach Nathan Buckley had kinder words for Thomas, who was selected at pick two in the 2005 national draft.
"'Daisy' has always played with passion and as a young player he embodied the new spirit of the sides that would win the flag in 2010 and play in the grand final of 2011," Buckley said.
"He was a big occasion player who often thrived on the MCG stage. He enjoyed the theatre. The crowds, the roar, the stakes, they seemed to inspire him.
"The game has since thrown its challenges at him and he is looking to start afresh but he shared in a history-making moment with us and will always be remembered for that. Everyone at Collingwood wishes him well."