The TV commercial, first broadcast in May, features chimpanzees dressed in tracksuits riding bikes and working on cars, with the strap-line "because you pay peanuts, we give you monkeys."
The Captive Animals' Protection Society organised a series of store protests and now Halfords has written to CAPS promising not to use chimpanzees in commercials again.
The chimp advert attracted 126 complaints to the Independent Television Commission (ITC), some from Halfords staffers offended at being branded as "monkeys."
Primate experts across the world condemned the advert and the cast and crew of the BBC drama Judge John Deed spoke out in opposition to it.
Craig Redmond, campaigns officer for the Captive Animals' Protection Society said:
"We are delighted that Halfords have responded to the massive opposition to the exploitation of animals in this way and hope that other companies will also take notice of this. There has been a worrying trend recently for advertisements to feature wild animals who suffer greatly in captivity, particularly great apes, dolphins and elephants."