Whole Foods shareholders have agreed to Amazon's proposed $13.7bn of the chain, paving the way for the e-commerce giant to move into bricks-and-mortar groceries.
Amazon said in June that it will pay $42 a share for Whole Foods, in a cash deal which will include the firm's debt.
High-end grocer Wholefoods, which has 466 stores, will provide Amazon with a new opportunity in the grocery market, and the tie-up has put traditional grocers on edge.
Shares in UK supermarkets fell when the news was announced as investors became concerned about the future of the traditional grocers.
Amazon has already started flexing its muscles in the grocery sector with the launch of its online delivery service Amazon Fresh, and the opening of a Amazon Go, a concept store in Seattle with no check-outs.
"Amazon can modernise and transform Wholefoods into a grocery retailer of the future, competing directly with incumbent supermarkets with multiple fulfilment channels," said Molly Johnson-Jones, senior analyst at GlobalData.
"Simultaneously, Amazon can continue to work on its other grocery propositions such as AmazonGo, Amazon Fresh, and Amazon Pantry with the added benefit and risk reduction of having Wholefoods in its portfolio of companies."
The deal now awaits regulatory approval, with both parties expecting it to close by the end of 2017.