All 189 signatories to the treaty unanimously approved the declaration on Friday night. The text also reaffirms the commitment of existing nuclear powers to reducing their arsenals.
But the future of that 2012 conference is already in doubt: General James Jones, the US national security adviser, said the US "will not permit a conference or actions that could jeopardise Israel’s national security".
US defends Israel
"We will not accept any approach that singles out Israel or sets unrealistic expectations," he said in a statement.
In a separate statement released on Saturday, Barack Obama, the US president, said he "strongly oppose[s] efforts to single out Israel."
Israel is one of only three states which never signed the NPT, the other two being India and Pakistan.
It is believed to have a nuclear arsenal, though it refuses to confirm or deny its existence.
An Israeli government official described the deal as "hypocrisy" because it makes no mention of other countries that have not signed the NPT.
"This accord has the hallmark of hypocrisy," the unnamed government official told the AFP news agency.
"Only Israel is mentioned, while the text is silent about other countries like India, Pakistan and North Korea, which have nuclear arms, or even more seriously, Iran, which is seeking to obtain them."
The 2012 meeting - on a "weapons of mass destruction"-free Middle East - could effectively force Israel to declare and dismantle its nuclear weapons program.
Israel has said it backs such an agreement in principle, but only after signing peace treaties with other countries in the region.
The US had initially sought to block the provision; Washington has long shielded Israel from pressure to disclose the details of its nuclear programme. But American diplomats eventually agreed to the provision to salvage the conference.
"The Arab group basically drew a line in the sand and said, this is as far as we can go in compromising. This language must stay, or we will not back the final document," Al Jazeera's Kristen Saloomey said, reporting from New York.
"[And] the United States was very interested in moving this agenda of non-proliferation forward."
Ellen Tauscher, the US under-secretary of state for arms control, said "the United States deeply regrets" that the draft pressures Israel to join the NPT.
If negotiators agree on a bargain, it would be the first successful NPT review meeting since 2000.