The vote Friday was 295-to-123, with Obama losing the support of 70 of his Democrats one day after Secretary of State Hillary Rodham Clinton made a last-minute plea for the mission.
The House vote has no immediate effect on American involvement in the NATO-led mission. However, it represents a repudiation of the commander in chief.
Shortly after that vote, the House turned back a Republican-led effort to cut off money for military hostilities in the Libyan war.
The vote was 238-180. The funding measure would have barred drone attacks and airstrikes but allowed the United States to continue actions in support of NATO.
The congressional action marked the first time since 1999 that either House has voted against a military operation. The last time was over President Bill Clinton's authority in the Bosnian war.
House Republican leaders pushed for the vote, saying the president broke the law by failing to seek congressional approval for U.S. action.
The 1973 War Powers Resolution states that the commander in chief must seek congressional consent for military actions within 60 days.
On the other hand, some Democrats accused the GOP of playing politics with national security.
Earlier in June, the House voted 268-145 to rebuke Obama for failing to provide a "compelling rationale" for the Libyan mission and for launching U.S. military forces without congressional approval.