Yushchenko draws his support from the west of the Ukraine, but pro-Russian Yanukovych's power base is the east of the country.
Council head Boris Kolesnikov said the legislative body can see no other way to defend the interests of the Donbass.
The decision comes despite a warning earlier from the National Security and Defense Council, headed by outgoing President Leonid Kuchma, to the country's eastern regions to back away from any moves toward autonomy.
Yanukovych today attended a meeting in Severodonetsk, eastern Ukraine, of leaders from eastern regions who have threatened autonomy if the election result is overturned. Yanukovych told the meeting that Ukraine is in danger of "collapse."
He urged calm and avoidance of bloodshed. "I call on you not to take any radical steps. I repeat, none," he said. "As soon as the first drop of blood is spilled we won't be able to stop that flow. It will be on the conscience of those people who provoked this situation.
In Kyiv, Yushchenko today said officials in eastern regions promoting autonomy pose a threat to Ukraine, and demanded a criminal investigation into their actions.
"That occurring today in the east of Ukraine is crime against Ukraine," Yushchenko said. "I address [my remarks] to jurists. I address [them] to the conscience of the prosecutor-general."
Representatives of the two rivals have opened talks to find a solution to the crisis, but President Kuchma says those talks are not going well.