US Defense Secretary Robert Gates made the announcement after meeting with Indonesia's President Susilo Bambang Yudhoyono on Thursday in the capital Jakarta.
Indonesia's special forces have concentrated on counterinsurgency issues in recent years, but were accused of major abuses in the former Indonesian province of East Timor in the late 1990s. East Timor has since become independent.
Several countries, including the US and Australia, suspended joint military training in the wake of the allegations, though Australia resumed training in 2005.
The US lifted an overall ban against training the Indonesian military in 2005, though it kept the restrictions against the Indonesian special forces — known as Kopassus.
International rights groups said members of Kopassus were linked to the disappearance of student activists in East Timor in 1997 and 1998 and were never held accountable.
In May, 13 US lawmakers sent a letter Thursday to Secretary of State Hillary Clinton and Gates. They said they worried about whether Indonesia will punish senior officers for past abuses.