The council adopted a resolution on Tuesday ordering a travel ban and freeze of assets on Major-General Gaffar Mohamed El-Hassan, a commander of the Sudanese air force; Sheikh Moussa Hilal, chief of the Jalul tribe in northern Darfur; Adam Yaqoub Shant, commander of the Darfur rebel army of the Sudan Liberation Movement; and Gabriel Abdul Kareem Badri, field commander of the National Movement for Reform and Development.
China and Russia had initially opposed the sanctions on Tuesday but in the end chose to abstain instead of casting vetoes.
Qatar also abstained, saying it did not see enough evidence that the four men were involved.
The Chinese and Russian ambassadors feared that the sanctions could complicate Darfur peace talks under way in Abuja, Nigeria.
The African Union and the Security Council have demanded that an accord be reached by this Sunday.
But they were appeased with a statement from the council, agreed to before the vote, expressing support for the talks.
According to the statement, the council "urges the parties to make speedy progress in concluding a Darfur peace accord".
The four men who face sanctions are a former commander of the Sudanese air force's western region, a militia leader who is accused of allowing some of the worst atrocities and two rebel commanders.
Decades of tribal clashes erupted
into full-scale violence in 2003
The sanctions are the first imposed by the UN Security Council since it adopted a resolution in March 2005 authorising an asset freeze and travel ban on individuals who defy peace efforts, violate international human rights law, or are responsible for military overflights in Darfur.
John Bolton, the US ambassador, said: "This resolution demonstrates that the Security Council is serious in its efforts to restore peace and security in the region."
"We regret that the vote today was not unanimous, but we do not think it will deter the Security Council from fulfilling its responsibility."
Decades of low-level tribal clashes over land and water in the Darfur region erupted into large-scale violence in early 2003 when ethnic African tribes took up arms, accusing the Arab-dominated central government of neglect.
The government is accused of responding by unleashing Arab tribal militias known as Janjaweed to murder and rape civilians and lay waste to villages - a charge it denies.