Obama issued a proclamation restoring benefits for the three countries under African Growth and Opportunity Act (AGOA), which was signed into law in 2000.
"Today's announcement is the result of rigorous review by the Obama Administration to determine whether Cote d'Ivoire (Ivory Coast), Guinea, and Niger have made progress in meeting AGOA's eligibility criteria," Trade Representative Ron Kirk said in a statement.
"We have seen progress in each of these countries, in conducting free and fair elections and taking other actions to promote democratic government and market-based economies."
Congress established AGOA with the goal of expanding U.S. trade and investment with sub-Saharan Africa and stimulating economic growth in the region.
The program, along with the Generalized System of Preferences, allows most goods produced in the AGOA region to enter the United States without duties imposed at the border.
Ivory Coast lost its eligibility in 2005 following five years of political unrest and armed conflict.
The five-month crisis ended when Gbagbo was ousted by forces loyal to Ouattara, who was then sworn into office.
Guinea lost its AGOA eligibility in 2010 as a result of a coup and other abuses, but later that year held its first democratic presidential elections since 1958.
Niger lost its benefits in 2009 after President Mamadou Tanja attempted to hold onto power following the end of his second term in office by dissolving the national government and changing Niger's constitution.
A military junta deposed Tanja and he committed to leaving power following democratic presidential elections.
Those elections took place, and President Mahamadou Issoufou was inaugurated in April 2011.
Last year, the United States imported about $163 million worth of goods from the Ivory Coast, $85 million from Guinea and $50 million from Niger.
(Reporting by Doug Palmer; Editing by Paul Simao)