"This is an natural disaster rattling through the grocery sector as well as the retail world", said Mark Hamrick, senior economic analyst for Bankrate.com.
Moody's lead retail analyst Charlie O'Shea said the deal could be "transformative, not just for food retail, but for retail in general".
Following Amazon's move to plant a bigger stake in the food-selling business, shares of Walmart tumbled 4.6%, making it the biggest loser in the blue-chip Dow Jones industrial average. On Friday, WalMart announced it is buying men's online clothing retailer Bonobos for $310 million.
Although Amazon has been dabbling in the fresh produce arena in certain American markets recently, the acquisition of Whole Foods has upset the traditional groceries industry and also impacted food supply companies. Firstly, don't forget that Whole Foods is a pretty trendy and high-end outlet with an organic focus.
The grocery chain, known for its organic options, had been facing increased pressure from rivals, including European grocery chain Lidl, which is planning to enter the East Coast market, along with Aldi and Trader Joe's. Customers are assigned a personal shopper who scours the aisles, purchases and delivers items from retailers like Whole Foods. Shoppers simply pick the items they want off the shelves and leave the store.
But if Amazon can be the one-stop shop for everything - groceries had been one of the key missing elements - customers would have even less of a need to go to Walmart or elsewhere.
"For the most part, it's too expensive for me to do all may shopping there", said Mary Funari, a Whole Foods shopper.
Drew Herdener, an Amazon spokesman, said in a statement the company has "no plans to use no-checkout technology to automate the jobs of cashiers at Whole Foods and no job reductions are planned".
In the United Kingdom, where there are Whole Foods stores, sell-offs wiped out almost $2billion (£1.5billion) from the value of stocks at grocers Tesco, Sainsbury's and Marks & Spencer, according to This Is Money.
"Amazon is an innovative company and we are excited about our partnership".
That was feeling of Taylor Malooly, 19, a University of Texas student at Whole Foods in Austin, who said a Whole Foods delivery service would have to be fast if he were to try it.
In an email to customers titled "exciting news", Whole Foods vowed to keep quality high.
"This will definitely make the market more competitive", she added.
The deal sent shockwaves across the food distribution market and beyond.
"This is going to have a profound effect on how convenient it will be for consumers to buy groceries", Smith said.
Whole Foods had been under pressure from activist hedge fund Jana Partners LLC prior to the announcement of Friday's deal, prompting it to overhaul its board of directors. It's also been testing automation technology at a Seattle convenience store that's now open only to Amazon employees.