With 90.03 percent of the votes counted Monday morning, Yushchenko won 54.08 percent of the votes, against 42.13 percent for Yanukovych in Sunday's election which witnessed 77.34 percent turnout.
Earlier Monday, Yushchenko claimed victory in the election, saying the nation was beginning a new political life.
But Yanukovych refused to accept failure and pledged to lead a tough opposition if he lost.
Yanukovych had defeated Yushchenko by a narrow margin in the November 21 run-off, but Yushchenko's supporters staged widespread demonstrations against electoral fraud.
The results were subsequently annulled by the Supreme Court, leading to Sunday's repoll.