Cooney, who turns 28 in September and played his 200th game last round against Adelaide, has signed until the end of 2015, meaning he is likely to finish his career as a one-club player.
While the 2003 No.1 draft pick had always indicated his preference was to stay with the Bulldogs, the amount of time taken to reach a new deal had prompted speculation that he could head elsewhere as a restricted free agent.
His decision to re-sign follows a rich vein of form from the player who won the 2008 Brownlow Medal, but fractured a kneecap late that season which has made it hard for him to recapture his best since.
But, after off-season treatment in Germany before this season, Cooney has regained his burst of speed and showcased his class this year.
In the past five rounds he has picked up 30 touches or more four times.
While he didn't match that tally against the Crows on Sunday, his 23-disposal, two-goal performance was a key to the Bulldogs' win.
Cooney's hot form has coincided with a form surge from the Dogs, with the club posting three wins and pushing last year's grand finalists Sydney and Hawthorn over the past five rounds.