Rio Tinto sponsors the AFL's Indigneous pathway program, and the league faced criticism over the partnership as other organisations acted to sever ties with the mining giant following the blast in May.
The destruction has prompted a senate inquiry, three Rio Tinto executives to resign and Reconciliation Australia to revoke the company's Elevate RAP (Reconciliation Action Plan) status.
This week the inquiry heard from the Puutu Kunti Kurrama and Pinikura Traditional Owners, who said the blast and subsequent loss of the significant rock shelters had caused "immense grief" for them.
Rio Tinto's partnership with the AFL, which funded three Indigenous football programs - the Flying Boomerangs, the Woomeras and the Footy Means Business program, was worth close to $1.5 million.
The partnership was up for renewal this year.
The decision to end the partnership came after the AFL's head of inclusion Tanya Hosch consulted with Indigenous people, including the league's own Indigenous Advisory Council.