The vote in the House of Representatives was 262-167 for the Colombia pact, 300-129 on Panama and 278-151 on the South Korea accord, the largest of the three.
Senators voted 83-15 for the Korean deal, while the Panamanian and Colombian accords were approved by margins of 77-22 and 66-33, respectively.
Voting on the pacts, negotiated by the Bush administration in 2006-2007, pitted proponents of free trade against union-backed lawmakers who warned of more jobs being shipped abroad.
In the end, Republicans, including many of the president's staunchest critics, supported the trade deals almost unanimously while many Democrats defied the White House and opposed them.
The Obama administration argued that these and other trade deals - the United States had 11 other pacts in effect with 17 countries prior to Wednesday's voting - will lead to rising exports and spur growth and job creation.
According to the White House and its pro-free trade allies, the pacts will help create 250,000 jobs and increase exports by some $13 billion. The pact with South Korea, the United States' seventh-biggest trade partner, will help create 70,000 jobs, advocates say.
Senate Minority Leader Mitch McConnell (R-Ken.) said before the vote that the pacts will reduce tariffs and other barriers to the entry of U.S. products and "will level the field" for U.S. companies and workers.
At a time when the country is saddled with unemployment of 9.1 percent, greater exports will create much-needed jobs, McConnell said.
But Sen. Sherrod Brown (D-Ohio) contended that the agreements are a mere continuation of the "failed model" represented by the 1994 North American Free Trade Agreement linking the United States, Mexico and Canada, saying they will offer "more of the same" and harm small business and U.S. workers.
Detractors in the House included Maine Democrat Mike Michaud, a former paper mill worker who said the trade deals will only cause more "devastation" to U.S. communities.
The Colombian agreement sparked the most heated debate, with Democrats denouncing violence against trade unionists in the Andean nation and Republicans pointing to Bogota's progress is boosting security and human rights protections.
Many Democrats rued the fact that even though Colombia pledged to take forceful action to protect unionists as part of a "labor action plan" announced at the White House in April, no reduction in violence needed to be shown before the trade pact was ratified.
"I find it deeply disturbing that the United States Congress is even considering a free trade agreement with a country that holds the world record for the assassinations of trade unionists," Rep. Maxine Waters (D-Calif.) said during the debate in the House.