The investors have criticized Whole Foods for its poor performance, and have suggested the chain could be merged with another grocer.
"This partnership presents an opportunity to maximize value for Whole Foods Market's shareholders, while at the same time extending our mission and bringing the highest quality, experience, convenience and innovation to our customers," John Mackey, Whole Foods' CEO, said in a statement.
Also, Wal-Mart has been successful with its so-called click-and-collect model, where shoppers order online but stop by the store to pickup their orders.
Amazon is often associated with great value while Whole Foods has often been called "whole paycheck," due to its higher priced organic goods.
"But Whole Foods is a store with generally very expensive real estate, and high prices, which is the opposite of what Amazon is all about, so it'll be interesting to see how Amazon brings Whole Foods into the fold and adapts to a completely different model." News that the e-commerce giant is buying Whole Foods sent grocery stocks reeling on Friday.