Merkel's office said she and Obama agreed on the "importance of a rapid ceasefire observed by both sides."
"Russia must first contribute by ensuring that the separatists in eastern Ukraine uphold the ceasefire," the German account of the call said.
The White House said the pair flagged the possibility of further costs being levied on Russia if it didn't cooperate.
"They stressed that Russia must take immediate steps to de-escalate the conflict in eastern Ukraine. The president and the chancellor agreed that the United States and Europe should take further coordinated measures to impose costs on Russia if it does not take steps toward de-escalation in short order," the White House said.
It comes shortly before Saturday's deadline for defining the conditions of a ceasefire between pro-Moscow rebels and Kyiv - a target agreed to earlier this week in a Berlin meeting between the foreign ministers of Germany, Ukraine, Russia and France.