The failure was due to a maintenance update and not a cyber attack, says newspaper.
The New York Times said access to its website is being fully restored after falling offline for about two hours on Wednesday.
NYT officials denied the failure was the result of a cyber attack, and said it happened because of an issue with a planned maintenance update.
Spokeswoman Eileen Murphy said: "We have no reason to believe that this was the result of a cyber attack.
"The outage occurred within seconds of a scheduled maintenance update being pushed out, and we believe that was the cause."
Readers were redirected to the NYT’s Twitter and Facebook accounts during the outage.
"Readers, don’t fret. If nytimes.com remains down, we are ready to tweet op-eds and editorials in 140-character increments," read the Twitter feed for the website’s opinion section.
Nytimes.com was brought down several times by Chinese hackers in January, prompting fears of another hacking success on Wenesday.
Incidentally, Wednesday also happened to be the 10th anniversary of the East Coast blackout, when a widespread power outage struck.
Earlier this week, security researchers said that the Chinese-based hackers, who were accused of a high-profile attack on the New York Times for four months, have come up with an improved version of malware.