The 15-nation council unanimously passed two resolutions which set up one new blacklist of individuals and organisations accused of links to al-Qaida and a second for those linked to the Taliban militia.
The two groups have until now been handled by the same sanctions committee. But the United States and some other major powers wanted to separate them to highlight the divide between al-Qaeda's global jihadist agenda and the Taliban's focus on Afghanistan.
The move makes it easier to add and remove people and entities from the sanctions lists. The council also established specific criteria for having an individual delisted. The vote was unanimous.
"It sends a clear signal that now is the time for the Taliban to come forward and join the political process," Mark Lyall Grant, the UK ambassador to the U.N., told the council.
The creation of two separate lists seemed to be an admission that, especially in the wake of Osama bin Laden's death, the relationship between the two organizations has changed since the sanctions regime was created in 1999.
"The link between al Qaeda and the Taliban has not disappeared, but it's not the same as in 1999," French Ambassador Gerard Araud told the council.
The two resolutions passed by the council give the Afghan government a greater role in determining who is on the Taliban sanctions list.
"From now on, the Afghan government has a visible and distinct role in the process of listing and delisting," German Ambassador Peter Wittig said.
Responding to pressure from the Afghan government, among others, the council last year created an ombudsman to review appeals from individuals who wanted to be delisted. This new resolution strengthens that position by, for the first time, allowing the ombudsman to make recommendations to the council on delistings, which the council can overturn only by consensus vote.
The United States is set to begin withdrawing troops from Afghanistan next month. In a statement, U.S. Ambassador Susan Rice said that the resolution "sends a clear message to the Taliban that there is a future for those who separate from al Qaeda, renounce violence and abide by the Afghan constitution."
The UN has been asked by the Afghan government o remove about 20 former Taliban figures from the list. It originally asked for 50 names to be considered, but withdrew many because paperwork to back up their cases was not available.
The sanctions committee is due to debate the remaining cases in mid-July.