The 29-year-old man suffered an ankle injury after he fell while allegedly attempting to roll out a banner on the building.
The activists, who occupied CBA cites across Australia, want the bank to rule out funding for coal mining near the Great Barrier Reef.
A female abseiler, who was also on the building, was taken away by police.
The man was taken to The Alfred Hospital in a stable condition, while the protest continued on Bourke Street.
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