"To get started, we're going to lower prices beginning Monday on a selection of best-selling grocery staples, including Whole Trade organic bananas, responsibly-farmed salmon, organic large brown eggs, animal-welfare-rated 85% lean ground beef, and more," Jeff Wilke, CEO of Amazon Worldwide Consumer, said in a release. "And this is just the beginning — we will make Amazon Prime the customer rewards program at Whole Foods Market and continuously lower prices as we invent together."
Whole Foods has more than 450 locations and is known for selling higher-priced, often organic, produce, while retailers like Wal-Mart have emphasized lower prices and savings for customers.
For example, bananas can cost 99 cents a pound at Whole Foods versus 49 cents at Wal-Mart.
"Over the longer term, I do see Amazon is going to be more competitive in this world," Joe Feldman, analyst at Telsey Advisory, said Thursday on CNBC's "Power Lunch." He did note that Wal-Mart and Costco's share price decline Thursday was "a bit of an overreaction" because of the difference in customer demographic.
Amazon closed down modestly amid a broader market decline, but held gains of 27 percent for the year. Whole Foods ended up slightly.
Of the six stocks listed above, only Wal-Mart and Sprouts have gained this year, up 13 and 17 percent, respectively.
Consumer staples fell 1.3 percent, the group's worst day since Nov. 30 and the worst performer in the S&P 500. Kroger was one of the biggest decliners in the stock sector.
— CNBC's Lauren Thomas contributed to this report.