Police were summoned to the scene at 9:42 p.m. on request from firefighters who were treating an unconscious man at the store, located at 230 Bay Place.
The customer had allegedly made physical contact with a store employee when the guard intervened, Whole Foods spokeswoman Beth Krauss said.
Oakland resident Zoe Marks, who witnessed the incident, says she couldn't believe her eyes.
"We saw a young man who was trying to buy groceries and engaged in some sort of verbal interchange with the checkout cashier," said Zoe Marks, of Oakland.
"There was confronted by the security guard, told to leave the premises and then actually physically accosted, thrown against a wall, and then told he had to go to customer service. He was trying to escape the security guard, thrown against the wall again. He ended up, at the end of the altercation, face down on the pavement in a pool of his own blood."
That guard has since been barred from working at Whole Foods in the future.
In an email to ABC7 News, Whole Foods says, as a result of the violent behavior of the security guard at Whole Foods Market Oakland, "We are replacing this security firm in the store. The new firm is A.G.S. Private Security, owned and operated by Ms. Gloria Lawrence of Concord."
The email went to say that Whole Foods is also working with all of the private security firms they contract with to, "reiterate and reinforce our expectations that they abide by our code of conduct."
"We are reviewing our internal processes and policies to evaluate opportunities for improvement. In addition, since our store opened we've worked hard to develop relationships with community organizations. In the coming days and weeks, we will reach out to these and other community partners to help us learn how we can continue to evolve our support for our diverse Oakland community."
Marks took pictures immediately after the incident of the young man on the ground that showed the man was bleeding from the head and face.
Marks said she and other customers called 911, while store employees appeared to do little, except to lock the front doors of the building.
"I don't think ending up face down unconscious on the pavement in a pool of your own blood and leaving the grocery store on a stretcher is ever justified," Marks said.
A Whole Foods spokesperson told ABC7 News "The graphic images circulating on Facebook and Twitter are disturbing to say the least. The security guard involved in the incident has been permanently removed from Whole Foods Market."
"Much of what's been reported about this incident has alleged that the use of an EBT card had a role in the altercation," said Whole Foods spokeswoman Beth Krauss. "We want to clarify that EBT cards are readily accepted forms of payment at all Whole Foods Market stores."
Whole Foods has also been addressing the incident with customers on their Facebook page.
Police confirm they are also investigating an assault at the Whole Foods, saying the injured man is in stable condition.