Parliament gave Yuriy Yekhanurov 289 votes on Thursday, well above the 226 he needed - just days after parliament had refused the same candidate.
The extra backing came after Yushchenko signed a formal truce with losing presidential candidate Viktor Yanukovych's Party of the Regions.
The president needed the extra votes to offset the defection of some of his Orange Revolution allies after the ouster of former Prime Minister Yulia Tymoshenko.
"It's time to bury the war hatchet and to forget where it lies," Yushchenko said before the vote. Later he said that a "unique understanding" had been found.
The parliamentary hall erupted into applause, and Yushchenko, who had come to the session to make one final plea, immediately stood up and warmly hugged Yekhanurov.
Yulia Tymoshenko was the Orange
Revolution's most popular figure
"We have passed through a difficult path of reconciliation of the political elite," Yekhanurov said after the vote.
The former governor from eastern Ukraine said he would unveil his plans for his new team next week in Dnipropetrovsk.
“We have no time to warm up,” he said, adding that at least one-third of his new appointments would be technocrats with no relation to politics.
Yushchenko dismissed Tymoshenko on 8 September - who had pleaded to return as prime minister - but Yushchenko stuck by Yekhanurov, an economist and moderate whom lawmakers called a neutral choice.
"This is the beginning of the aggravation of the political crisis because Tymoshenko's proposal about cooperation and mutual understanding ... was ignored," said lawmaker Andriy Shkil from Tymoshenko's bloc.
He also noted that "Yanukovych, recently he was a bandit, a criminal", referring to allegations that the Orange Revolution team had lobbied against their one-time enemy last year.
The new vote came after a series of consultations between Yushchenko and parliamentary faction leaders.
Yanukovych's Party of the Regions gave Yekhanurov 50 votes, enough to push him over the required limit. In Tuesday's vote,
Yanukovych's party had abstained.
Yushchenko sacked Tymoshenko's government after members of the Orange Revolution team began bickering over corruption accusations.
While Yushchenko has championed the dismissals as a fresh start, the near daily accusations between the former allies and the president's inability to get a new cabinet approved have given the appearance of bringing government work to a
halt in this nation of 48 million.