And it's anyone's guess as to how long the so-called the shock waves among retailers will continue.
On Friday, shortly after Jeff Bezos and his team announced Amazon's big vision to shake up the grocery industry and acquire grocer Whole Foods, these big-box retailers' stocks tumbled, with shares of Target falling more than 10 percent at one point.
Traditional grocers such as Kroger and Supervalu also took significant hits on Friday but were not trading nearly as low by Monday morning. In fact, shares of Kroger were inching back into green after tanking more than 15 percent in a day.
Deutsche Bank on Monday lowered its rating for Costco specifically to hold from buy, saying the competitive advantage from its food business is at risk due to Amazon.
"The WFM acquisition represents a game changer with COST's competitive moat in grocery under greater threat while its digital platform lags peers, putting membership renewal at risk for decline," Deutsche Bank analyst Paul Trussell wrote in a note to clients.
"The pipeline of positive catalysts has played out and the competitive backdrop is intensifying with AMZN ... accelerating in-store and online efforts and innovation."
The online threat is "real and intensifying" for some of the biggest names in the retail sector, Trussell went on.
Representatives from Target, Wal-Mart and Costco didn't immediately respond to requests for comment.
Meanwhile, Amazon's stock jumped to a fresh all-time high of $1,017 a share Monday.
"I think this [deal] is certainly a game changer," David Lebovitz, a global market strategist for JPMorgan, said during an interview on CNBC Monday morning.
Amazon's strategy will make retailers like Target and Wal-Mart ask themselves questions about where retail is headed, Lebovitz said. But he warns investors to not become "too wrapped up" in the immediate deal aftermath and how securities have reacted in the days following.
Wall Street needs to think more about what this Amazon-Whole Foods buy is going to look like long term before jumping to conclusions, he added.
"If I was a shareholder of Target I would be terrified," Tom Forte, managing director of Maxim Group, told CNBC in an interview on Friday. "Grocery was just one category for [Amazon] to expand into."
—CNBC's Tae Kim and Michael Bloom contributed to this report.