The new sanctions prevent 11 entities and individuals linked to the missile program from using the US banking system.
The move came after international nuclear sanctions on Iran were lifted as part of a deal hailed by President Barack Obama on Sunday as “smart”.
Four American-Iranians were also freed in a prisoner swap as part of the deal.
Among them was Washington Post reporter Jason Rezaian – whom President Obama described as “courageous”. A fifth American was freed separately.
Rezaian and two of the others freed flew to a US base in Germany via Geneva for medical evaluation.
Another, Nosratollah Khosravi-Roodsari, did not fly out with the others, US officials said. A fifth man, Matthew Trevithick, was freed in a separate process.
The US said it had offered clemency to seven Iranians being held in the US for sanctions violations.
Negotiations in December over the prisoner exchange delayed the US Treasury’s imposition of the latest sanctions.
They were only announced once the plane containing the former prisoners had left Iran, reports said.
They were triggered by Iran conducting a precision-guided ballistic missile test capable of delivering a nuclear warhead last October, violating a United Nations ban.
“Iran’s ballistic missile program poses a significant threat to regional and global security, and it will continue to be subject to international sanctions,” said Adam J Szubin, US acting under-secretary for terrorism and financial intelligence.
Moments later, President Obama hailed the nuclear deal, which is being implemented following verification by the International Atomic Energy Agency (IAEA) that Iran had restricted its sensitive nuclear activities.
“This is a good day because once again we’re seeing what’s possible with international diplomacy,” Mr Obama said.
“For decades,” he said, “our differences meant our governments almost never spoke – ultimately, that did not advance America’s interests.”
The deal meant “Iran will not get its hands on a nuclear bomb”, he said.
He said differences with Iran remained, and the US would “remain steadfast in opposing Iran’s destabilising behaviour elsewhere” – such as its missile tests.
And he defended a separate settlement at an international legal tribunal which will see the US repay Iran $400m (£280m) in funds frozen since 1981 plus a further $1.3bn in interest – saying there was no point “dragging this out”.
Earlier, Iranian President Hassan Rouhani said the nuclear deal opened a “new chapter” in the country’s relations with the world.
The deal has been welcomed by many governments, the UN and EU – but disparaged by some US Republicans and Israel, which says it allows Iran to continue to “spread terror”.
What are the sanctions?
Nuclear sanctions have been in place since 2006, on top of other sanctions stretching back decades:
- The economic sanctions being lifted now were imposed progressively by the US, EU and UN in response to Iran’s nuclear programme
- The EU is lifting restrictions on trade, shipping and insurance in full
- The US is suspending, not terminating, its nuclear-related sanctions; crucially, Iran can now reconnect to the global banking system
- The UN is lifting sanctions related to defence and nuclear technology sales, as well as an asset freeze on key individuals and companies
- Non-nuclear US economic sanctions remain in place, notably the ban on US citizens and companies trading with Iran, and US and EU sanctions on Iranians accused of sponsoring terrorism remain in place
A flurry of Iranian economic activity is anticipated:
- Nearly $100bn (£70bn) of Iranian assets are being unlocked
- Iran is expected to increase its daily export of 1.1m barrels of crude oil by 500,000 shortly, and a further 500,000 thereafter
- Iran is reportedly poised to buy 114 new passenger planes from the Airbus consortium
The prospect of Iran doubling its crude oil exports has contributed to the continuing fall in the oil price. Benchmark Brent crude closed below $29 (£20.3) on Friday.
Share prices in Saudi Arabia, the Arab world’s largest stock market, fell more than 6% following the lifting of sanctions.
The IAEA said it had installed a device at the Natanz plant to monitor Iran’s uranium enrichment activities in real time, in order to verify that uranium enrichment levels were kept at up to 3.67% as agreed in the deal with world powers.
As part of the deal, Iran had to drastically reduce its number of centrifuges and dismantle a heavy-water reactor near the town of Arak, both of which could be used in creating nuclear weapons.
Iran has always maintained its nuclear programme is peaceful, but opponents of the deal say it does not do enough to ensure the country cannot develop a nuclear bomb.