"This is a last chance", Trump said in a statement.
If Trump had not signed those waivers, sanctions would automatically be reinstated, putting the United States in contravention of the deal's terms and likely spelling the end of the 2015 pact.
"This is a last chance". Also on Friday, the United States imposed separate sanctions on a dozen Iranian individuals and Iranian entities.
In November, the body again said Iran was in compliance.
Mr Trump has repeatedly criticised the accord, while Iran has accused the USA of failing to comply with it.
Iran also rejected any changes to its nuclear deal with world powers.
Iran has complained that USA sanctions not connected to nuclear activity have effectively cancelled out any financial benefits it expected from the 2015 deal.
One senior administration official said Trump would be open to remaining in a modified deal if it were made permanent.
"My policy is to deny Iran all paths to a nuclear weapon - not just for ten years, but forever", Mr Trump said.
Also slapped with the penalties were the Iranian Revolutionary Guards Corps' Electronic Warfare and Cyber Defense Organization, and Chinese national Shi Yuhua.
That in turn would cause crude prices to rise by $5 a barrel, Citigroup wrote, "as customers losing oil under USA pressure scramble for replacements at a time when OPEC and other producers have put a lid on their output". He is the brother of the speaker of the Iranian parliament, Ali Larijani, the officials said. Work already has begun on this front, the official said.
Specifically, Trump had until Friday to decide whether to continue waiving 2012 sanctions that cut off Iran's central bank from the global financial system, with a host of other, similar deadlines following over the next week.
The U.S. will negotiate the new parameters with its European allies only, not Iran, according to the official.
"In what we heard yesterday, I don't see any invitation for Iran to enter dialogue", he said.
"We will continue to work together with global community against these USA steps", he added. Noncertification to Congress does not affect the actual accord, however. And by the way, it has been endorsed by the U.N. Security Council. It also could hand Iran a pretext to start limiting United Nations inspections or restart its nuclear program.
The announcement came as the Treasury Department placed sanctions on 14 individuals and entities for alleged offenses unrelated to Iran s nuclear industry.
Trump wants them to help the USA devise a new agreement created to prevent Iran from escalating nuclear activity again next decade, as permitted under the 2015 arrangement reached by President Barack Obama.
European signatories to the deal have pressured the United States to stick to the accord.
Trump laid out conditions to keep Washington in the deal. It's keeping Iran's nuclear program in check.
Trump told Macron that Iran had to stop its "destabilizing activity" in the region, the White House said. "Rather than repeating exhausted rhetoric, USA must bring itself into full compliance - just like Iran".
The sanctions with the most political repercussions are against the administrative head of Iran's judiciary, Sadegh Amoli Larijani.
He was among those calling for a crackdown following a recent spate of anti-government protests across Iran.
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