The approval came less than two weeks after hundreds of Correa supporters stormed congress, battled police on the streets and forced lawmakers to evacuate the building to demand the referendum be approved.
Dozens of opposition lawmakers walked out in protest on Tuesday after demanding broad changes to the plan, but the legislature made only minor rewrites.
Correa's movement has no formal representatives in congress, but the former economy minister appeals to the public with his vows for a "citizen's revolution" in a country where instability has toppled three presidents in a decade.
"This is a victory for the people," Gustavo Larrea, the interior minister, told reporters after the decision.
Larrea said the government sees no significant changes in congress-approved reforms to the referendum plan.
Elected in November, Correa has rattled Wall Street and Washington with pledges to restructure debt and end a lease allowing the US military to use an air base and by fostering ties with Hugo Chavez, the Venezuelan president.