The FTC conducted an investigation to gauge whether the merger would decrease competition under federal regulations, Bruce Hoffman, acting director of the Federal Trade Commission's Bureau of Competition, said in a statement Wednesday. It ultimately decided not to pursue the matter further.
Amazon and Whole Foods did not immediately respond to a request for comment.
Whole Foods hours before the FTC's announcement.
The two companies expect to finalize the agreement during the second half of the year. However, source familiar with the matter told CNBC the deal could happen sooner rather than later.
Amazon announced its intention to buy Whole Foods for $42 per share in June. The price represented a 27 percent premium at the time.
-CNBC's Lauren Thomas contributed to this report