Under the all-cash deal, Amazon will acquire the Texas- based champion of organic and specialty food for $42 a share. Whole Foods traded in the mid-$30 range for May and the first part of June.
Whole Foods, which has faced pressure from activist investors, will continue to operate stores under its brand and will be led by co-founder and chief executive John Mackey, the companies said.
"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," Mackey said.
The hedge fund said the company was undervalued and needed to overhaul its operations and consider "strategice alternatives," a term usually used to indicate a sale.
The deal is the latest big move for Amazon and its charismatic chief executive Jeff Bezos, who grew Amazon from a small online bookseller in the 1990s into a global retail behemoth that delivers a wide range of goods and creates award-winning entertainment broadcasts.
"Millions of people love Whole Foods Market because they offer the best natural and organic foods, and they make it fun to eat healthy," Bezos said.
Trading of Whole Foods shares was halted, while Amazon rose 2.0 percent to $983.40 in pre-market trading.
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