Commission chief Yaroslav Davydovich announced on Monday that Yushchenko took 51.99% of all votes cast, while former prime minister Viktor Yanukovich took 44.2%.
Davydovich added that just over 77% of the electorate took part in the ballot and that well over two million votes separated the candidates.
"This is the happiest day of my life," Petro Poroshenko, a deputy in Yushchenko's Our Ukraine bloc and one of the four leading candidates for the post of prime minister, said.
"Ukraine has proved that it is a European country... A new country and a new government were born today," he added.
However. Yanukovich insisted that he would keep up a legal challenge to the decision and Nester Shuffrich - a Yanukovich representative at the commission - promised to appeal the result in the Supreme Court.
"Unfortunately the election results have been determined with violations of the election law and the constitution," he said. "We will discuss these violations tomorrow or the next day at the Supreme Court."
Nevertheless, the announcement paves the way for parliament to set a date for Yushchenko's inauguration, putting an end to weeks of political turmoil.
The 26 December rematch between Yushchenko and Yanukovich was set after the Supreme Court threw out results of a 21 November runoff - which election officials said was won by Yanukovich - because of massive fraud.
Many in Kiev speculate that the inauguration could take place on Friday - New Year's Day in the Julian calendar used by the Orthodox Church to which most Ukrainians adhere.