The sub-heading read "Cooking the Books for the White House" and said Petraeus is a "military man constantly at war with the facts".
confirmed it paid $65,000 (£32,500), according to a report on Reuters, whereas the normal rate of an ad of that size and type in the paper is around $181,000.
Rival paper The New York Post, owned by Rupert Murdoch's News Corporation, ran a story yesterday, headlined "Times Gives Lefties a Hefty Discount for 'Betray Us' Ad", which questioned why the basic rate was discounted.
Subsequently, Republican Presidential candidate Rudolph Giuliani sought and received space in today's (Friday) edition of The Times for an ad in which he praises Petraeus.
Giuliani and a group of conservative Republicans said the rate charged to MoveOn.org was favouritism and condemned the ad, saying it questioned Petraeus's integrity and was unpatriotic.
But Times spokeswoman Catherine Mathis denied the discounted rate charged to the anti-war group indicated political bias.
She said: "We do not distinguish the advertising rates based on the political content of the ad. The advertising [team] did not see the content of the ad before the rate was quoted."