"I am proud to declare that the United States formally recognizes the Republic of South Sudan as a sovereign and independent state upon this day, July 9, 2011," Obama said in a statement.
South Sudan's independence comes after more than 50 years of conflict between the southern rebels and successive Khartoum governments that left the region in ruins, millions of people dead and a legacy of mutual mistrust.
The 2005 comprehensive peace agreement (CPA) that finally ended the conflict, and which was signed under intense pressure from foreign countries, particularly the United States, Britain and Norway, paved the way for a referendum on southern independence in January. Around 99 percent of southerners voted to split from the north.
Earlier Saturday, South Sudan's parliament speaker, James Wani Igga, proclaimed the state's independence, marking the birth of the world's newest nation and splitting Africa's largest country in two.
Obama said he was confident that the bonds of friendship between South Sudan and the United States will deepen in the years to come.
"As Southern Sudanese undertake the hard work of building their new country, the United States pledges our partnership as they seek the security, development and responsive governance that can fulfill their aspirations and respect their human rights," he said.
Obama added that South Sudan's independence marked "another step forward in Africa's long journey toward opportunity, democracy and justice."
In a separate statement, Secretary of State Hillary Clinton commended the Government of Sudan on its decision to be the first to recognize South Sudan's independence.
"By continuing on the path of peace, the Government of Sudan can redefine its relationship with the international community and secure a more prosperous future for its people," Clinton said.