Three exit polls gave him a 15 to 20 percentage point lead over pro-Russian Prime Minister Viktor Yanukovych. The official count gave the Western-leaning Yushchenko a narrower 52.4 to 43.8 percent lead with ballots from 97 percent of the precincts counted in Sunday's election.
Results were trickling in slowly from two regions — Luhansk and Mykolaiv — both in pro-Yanukovych territory in eastern Ukraine. Central Election Commission chairman Yaroslav Davydovych appealed to election workers to do their jobs.
"Put political issues aside. The state is waiting for results," he said.
Yushchenko claimed victory Sunday's voting, but Yanukovych had not yet conceded defeat.
"Now, today, the Ukrainian people have won. I congratulate you," Yushchenko told a jubilant crowd in Kiev's Independence Square, the center of massive protests following the Nov. 21 presidential runoff that was annulled after fraud allegations.
"We have been independent for 14 years but we were not free," Yushchenko said. "Now we can say this is a thing of the past. Now we are facing an independent and free Ukraine."
Still, he was not taking chances. He called his supporters back out onto the square on Monday afternoon to defend the election victory, and asked their help in what he called the main task facing the nation: forming a government that would be trusted.
Some 12,000 foreign observers had watched Sunday's unprecedented third round to help prevent a repeat of the apparent widespread fraud on Nov. 21 that sparked massive protests after Yanukovych was declared the winner.
Both campaigns complained of violations, but Central Election Commission chairman Yaroslav Davydovych said neither the candidates nor their official representatives had lodged protests. Monitors said they'd seen far fewer problems this round, when 77.22 percent of registered voters turned out.
"This is another country," said Stefan Mironjuk, a German election monitor observing the vote in the northern Sumy region. "The atmosphere of intimidation and fear during the first and second rounds was absent ... It was very, very calm."
The new atmosphere was reflected in the comparatively small number of Yushchenko backers who poured into the square to hear his victory speech — in contrast with the tens of thousands who had thronged it earlier in the crisis.
About 5,000 applauded and set off fireworks. They waved bright orange flags — his campaign's emblematic color — and clasped hands and danced.
"Today we began to live! Today, we rose off our knees and showed ourselves and the world that our future can't be dictated to us. We will dictate it," said Olga Drik, 21, a Kiev student, who had covered her purse in orange ribbons.
Earlier, Yushchenko told journalists and others crammed into his orange-bedecked campaign headquarters that Ukraine was beginning "a new political life" that would include neither current President Leonid Kuchma nor Yanukovych, the prime minister and candidate whom Kuchma had hand-picked as his successor.
"I am convinced that it is fashionable to be a citizen of Ukraine. It is stylish. It is beautiful. Three or four months ago, few people knew where Ukraine was; today, almost the whole world starts its day from thinking about what is happening in Ukraine," Yushchenko said.
Even before the exit poll results were announced, a glum-looking Yanukovych told reporters that "if there is a defeat, there will be a strong opposition." But he did not concede and hinted he would challenge the results in the courts.
"We will defend the rights of our voters by all legal means," he said.
Voters faced a crucial choice at the election. Ukraine, a nation of 48 million people, is caught between the eastward-expanding European Union and NATO, and an increasingly assertive Russia, its former imperial and Soviet-era master.
Yushchenko, a former Central Bank chief and prime minister, wants to bring Ukraine closer to the West and advance economic and political reform. The Kremlin-backed Yanukovych emphasizes tightening the Slavic country's ties with Russia as a means of maintaining stability.
The political crisis has also cast a spotlight on the rift between Ukraine's Russian-speaking, heavily industrial east and cosmopolitan Kiev and the west, where Ukrainian nationalism runs deep. Yanukovych backers fear discrimination by the Ukrainian-speaking west, and some eastern regions briefly threatened to seek autonomy if Yushchenko won the presidency.
Yushchenko, whose face remains badly scarred from dioxin poisoning he blamed on Ukrainian authorities, has built on the momentum of round-the-clock protests that echoed the spirit of the anti-Communist revolutions that swept other East European countries in 1989-90.
"Thousands of people that were and are at the square were not only waiting for this victory but they were creating it," Yushchenko said. "In some time, in a few years, they'll be able to utter these historic words: Yes, this is my Ukraine and I am proud that I am from this country."