Thomas, 26, who was drafted by the Magpies at No.2 in 2005 under Malthouse, is looking to reignite his career after being restricted to just five AFL games this season by ankle injuries.
Ankle problems also kept him below his best last year, after fine seasons in 2010, when he was third in Collingwood's best and fairest in their premiership year, and 2011, when he earned All Australian selection.
"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 have 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."
Malthouse said Thomas gives the Blues added versatility.
"Dale is quick, hard at it, has a real presence about him, and will give us a real variety in positional play," the veteran coach said.
"He's been successful in being part of a premiership side, part of many finals campaigns and he brings to us a personality that will blend in very well with our current group."
Magpies coach Nathan Buckley said Thomas embodied the spirit of the club's 2010 premiership side, had always played with passion for Collingwood and thrived on big MCG crowds and big occasions.
"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," Buckley said.
Thomas kicked 121 goals in his 157 Collingwood games.
Magpies recruiting manager Derek Hine said Thomas' injury issues contributed to their decision not to match Carlton's offer.
"His ankle has obviously caused him some problems over the last year or two but we hope he finds his way back as a player," Hine said.