The deal between the world's top economy and Asia's fourth largest will boost trade by billions of dollars and create tens of thousands of jobs, the two sides say, making it one the biggest deals of its kind.
"The U.S.-Korea agreement is a landmark deal with an important ally," U.S. Trade Representative Ron Kirk said in a statement hailing the accord as the most significant U.S. free trade pact in 20 years.
"Starting today, Korea's doors are wide open for Made-In-America exports that will support well-paying jobs here at home," Kirk said.
The deal has provoked outbursts of violence in South Korea's parliament and street protests, mostly by farmers, including a small demonstration in the capital on Thursday.
The leader of the main opposition party, Han Myung-sook, this week backed down from a vow to repeal the deal altogether, saying she only wanted parts of it renegotiated.
Experts doubt major changes to the deal will be enacted.
U.S. President Barack Obama and South Korean President Lee Myung-bak spoke by telephone and praised the pact as symbolic of a strengthening of their alliance, the presidential Blue House in Seoul said in a statement.
"The South Korea-U.S. FTA is a high-standard treaty that will become a good model of global free trade," Lee was quoted as telling Obama.
Autos, investment troubles
The pact, which was signed in 2007 and finally approved by both countries in late 2011, immediately eliminates 80 percent of South Korea's duties on U.S. manufactured goods and nearly two-thirds of its duties on U.S. farm products.
In Seoul, shoppers felt the immediate impact, with bottles of Californian wine and citrus fruit flying off the supermarket shelves at up to a 20 percent off less than before.
South Korea is the United States' seventh-largest trading partner and has an economy valued at $1 trillion dollars. The pact's tariff cuts are expected to boost U.S. exports to Korea by $10 billion to $11 billion, helping to support 70,000 jobs.
The agreement mostly negotiated by the administration of former U.S. President George W. Bush and former South Korean President Roh Moo-hyun also opens up more of South Korea's large services market to U.S. companies and has new protections for exporters, investors, and intellectual property rights holders.
Lee's decision shortly after taking office in 2008 to reopen South Korea's market to U.S. beef triggered massive protests that caused the new president's popularity to plummet.
Within the United States, opposition from Obama's fellow Democrats prompted Obama to renegotiate the deal in late 2010 to get a better deal for U.S. automakers.
Ford Motor Co. and union groups complained the original pact failed to tear down longstanding "non-tariff" barriers to South Korea's auto market.
Once finally submitted to Congress, the pact sailed swiftly through both the House of Representatives and Senate.
Lee's party rammed the agreement through the South Korean parliament in November, despite an attempt by an opposition member to disrupt the vote by detonating a teargas canister.
In February, nearly 100 South Korean parliamentarians, most from the opposition, wrote to Obama to urge him not to implement the agreement without making a number of changes, particularly in the section governing bilateral investment disputes.
South Korea will elect a new parliament next month, and a new president in December.