There had been much speculation in recent days over whether Finnis would accept the position, and after a long period of negotiation the man who has headed the AFLPA since taking over from Brendon Gale in 2009 has decided to make the move.
Finnis is expected to start his new role in April once the review of equalisation policies and player payments is finished.
"It has been an absolute privilege to serve the players, who are not just elite professional athletes but fine young men," Finnis said on Tuesday.
"The focus of the Players' Association has been to champion the interests of the players and the game.
"This has not always been easy, popular or without conflict but hopefully people will respect the association for the manner it represents its members, always with the long-term best interests of the game at heart.
"I have had the opportunity to work with the leaders of this generation of players – people like Brendon Gale, Peter Bell, Joel Bowden, Brett Burton, Luke Power, Adam Goodes, Luke Ball and Matthew Pavlich and many others who have been committed to enhancing the lives of players and growing the game."
AFLPA president Luke Ball said the board accepted the resignation of Finnis with sadness.
"But we are also proud that the leaders of the PA consistently move on to leadership positions within the industry.
"Matt's contribution to the association over nine years of service has delivered a great legacy, and present and future players will benefit from his work."
St Kilda had been searching for a new CEO since Michael Nettlefold announced he was stepping down in September last year.
The club's chief operating officer, Terry Dillon, has been serving as acting chief executive during the search for Nettlefold's replacement.
President Peter Summers said Finnis impressed the club board from day one of the recruitment process.
"He is a highly respected figure in the football industry and brings the skill set the club was looking for in its new CEO," Summers said.
"Matt is a person of great integrity and professionalism and he has helped build the Players' Association into a financially strong and powerful organisation.
"The calibre of the candidates was of the highest quality and it took a lengthy and rigorous process to reach our final outcome."
A lawyer by profession, Finnis is taking one of the toughest jobs in the game.
The Saints are battling to build their revenue in the face of poor returns from matches at Etihad Stadium.
Making matters worse, they are set to struggle on the field for the next couple of seasons while they rebuild their list under new coach Alan Richardson.
At the same time, tensions continue to simmer over the club's decision to leave its old home ground at Moorabbin and establish a training base at Seaford.
Finnis lives in the bayside suburb Beaumaris, which is not far from Seaford and is considered part of St Kilda's heartland.
General manager of player relations Ian Prendergast is seen as a likely replacement as AFLPA chief, while Joel Bowden has reportedly expressed interest in returning to the Players' Association.
Bowden, who was president of the AFLPA until his retirement in 2009, joined the AFL in 2012 as game analysis manager and will sit on the Match Review Panel this season.