Metropolitan Transit Authority spokesman Kevin Ortiz said Tuesday that Amazon had decided to end the promotion, which includes seat wraps on one train and 260 subway station posters.
Amazon did not immediately respond to a request for comment.
The ads promote a new series that depicts an alternate reality in which Germany and Japan won World War II and occupy parts of the United States.
The advertisements featured a refashioned American flag with Nazi Germany's imperial eagle as well as symbols incorporating elements of the Japanese rising sun.
Similar ads in the London subway featured the Statue of Liberty giving a Nazi salute in front of the New York skyline; it's unclear whether those have been pulled as well.
Some people in New York had complained that the advertisements were offensive to those whose relatives were brutalized by the World War II regimes.
"I shouldn't have to sit staring at a Nazi insignia on my way to work," Ann Toback, executive director of a Jewish cultural and social and economic justice organization, told the Gothamist website.
Ortiz said that only one complaint had come into the MTA offices as of Tuesday morning, but plenty of complaints were evident on social media.
Critics accused the MTA of hypocrisy for allowing the show promotions while previously rejecting ads "pro-Israel, anti-jihad" ads proposed by Pamela Geller's American Freedom Defense Initiative, ads promoting underwear for menstruating women and those agitating on behalf of an increase in the minimum wage.
Ortiz said the ads didn't violate the agency's neutrality standards and so had to be allowed.
"Unlike CNN, the MTA is a government agency and can't accept or reject ads based on how we feel about them," he said in an email.
Among other things, the standards approved in April ban political and false or misleading ads, sexually oriented material, ads that promote smoking, "material the display of which the MTA reasonably foresees would imminently incite or provoke violence" and any ad that "demeans or disparages an individual or group of individuals."
The campaign was scheduled to end December 14.