The newspaper aired a 30-second clip, entirely in black and white, in one of the commercial breaks during the 89th Academy Awards last night.
The advert flashes a series of conflicting statements, and voices taken from news broadcasts, which all start with the three words: “The truth is.”
“The truth is the media is dishonest," reads one statement, in a clear reference to Donald Trump.
It finishes with the statements: “The truth is hard to find, the truth is hard to know, the truth is more important now than ever.”
The Oscars attracts a TV audience numbering tens of millions, with 34 million people tuning in to watch last year.
The slot would have cost between $2.15 million and $2.5 million, according to data from Advertising Age quoted by Associated Press.
Branding executive David Rubin told CNN: “The idea is to be a part of that discussion about what does it mean to find the truth.
“What does that mean in a world of ‘fake news’? And what is the role of journalism and journalists in that process, and what is the role of the reader in supporting that journalism?
“We think it's a great metaphor for how hard it is on a regular basis to understand the truth.
“That leads into the role that we think journalism can play in helping you cut through that clutter and make your own sense of what's going on in the world.”
The TV campaign will also appear in print form and run on billboards in New York, Los Angeles, Washington DC and San Francisco.
It was the first TV advert since The Weekender commercials of 2009.
Mr Trump tweeted yesterday: "For first time the failing @nytimes will take an ad (a bad one) to help save its failing reputation. Try reporting accurately & fairly!”
The previous day he wrote: “FAKE NEWS media knowingly doesn't tell the truth. A great danger to our country. The failing @nytimes has become a joke. Likewise @CNN. Sad!”
Online audio book service Audible also ran a politically-charged advert.
Actor Zachary Quinto read a passage from the novel 1984, which some also interpreted as a criticism of the US president.
He reads how "most of what" protagonist Winston Smith had been told about foreigners “were lies”.
Join our new commenting forum
Join thought-provoking conversations, follow other Independent readers and see their replies