Sprouts fell nearly 10 percent, Supervalu lost more than 2 percent and Target fell 1 percent. Wal-Mart closed about three-fourths of a percent lower. Kroger trimmed losses to close 0.1 percent lower, while Costco recovered losses to close 0.07 percent higher.
The six stocks have erased nearly $12 billion from their combined market capitalization since Wednesday's close, the day before Amazon announced it would complete its deal to buy Whole Foods Market on Monday and cut prices on many products, including bananas, organic avocados and organic Fuji apples.
On Monday, the price of an organic avocado at a Whole Foods location on New York's Upper East Side was $1.99, down from $2.99, CNBC found. The price of organic Fuji apples fell to $1.99 a pound from $3.49 a pound at that store.