The indigenous player's last season in the top flight Australian Rules competition was harrowing, as crowds across the country jeered him whenever he touched the ball.
The saga stoked a fierce debate as to the motivations behind the booing, and the AFL was slow to brand it racist.
Coinciding with the release of a documentary on Goodes's final years in the game, the AFL said it had failed the footballer, who was named Australian of the Year in 2014 for his community work.
"We apologise unreservedly for our failures during this period," the AFL said in a statement on Friday.
"Failure to call out racism and not standing up for one of our own let down all Aboriginal and Torres Strait Islander players, past and present.
"Our game is about belonging. We want all Australians to feel they belong and that they have a stake in the game.
"We will not achieve this while racism and discrimination exists in our game."
An outspoken activist for Aboriginal affairs, Goodes was racially abused by a 13-year-old fan during a 2013 match against Collingwood Magpies and pointed out the girl to security, who had her ejected from the match.
Two years later, conservative pundits and media commentators referred back to that incident and said Goodes had brought the booing on himself.
The AFL has worked hard to stamp out racism on and off the field but Aboriginal Australian footballers still occasionally suffer racist taunts from the terraces and on social media.
(Reporting by Ian Ransom; Editing by Nick Mulvenney)
