Whole Foods Market had sought $45 per share from Amazon but settled for $42 per share, which the e-commerce giant said was its "best and final offer".
Amazon had initially offered $41 in May, Whole Foods said in a regulatory filing on Friday.
Amazon also told Whole Foods that it was considering other opportunities in case the offer was turned down.
The company also asked Whole Foods not to approach other potential bidders while they were engaged in talks.
Amazon said in June it would buy Whole Foods for $13.7 billion, in a deal that could turn the high-end grocer into a mass-market merchant and upend the already struggling U.S. retail industry.