In their hour-long conversation, Vladimir Putin said Moscow-Washington relations should not suffer.
Russian troops have taken de facto control of Crimea following the fall of Ukraine’s pro-Moscow President Viktor Yanukovych.
The crisis has led to a boycott by many foreign dignitaries of the Sochi Winter Paralympics, which open on Friday.
Barack Obama stressed to Vladimir Putin that Russia’s actions in Crimea were a violation of Ukrainian sovereignty, the White House said in a statement.
The US president said there was a solution available that suited all parties, involving talks between Kiev and Moscow, international monitors in Ukraine and Russian forces returning to their bases.
For his part, Vladimir Putin said US-Russian “relations should not be sacrificed due to disagreements over individual, albeit extremely significant, international problems”, the Kremlin said.
It was Barack Obama and Vladimir Putin’s second telephone call concerning Ukraine in less than a week.
It comes after the EU and US joined Ukraine’s government in condemning as “illegal” a move by the Crimea region to set up a referendum to endorse joining Russia.
The Crimean parliament on Thursday said it had decided “to enter into the Russian Federation with the rights of a subject of the Russian Federation” and asked President Putin “to start the procedure”.
Crimea – whose population is mostly ethnic Russian – earlier set a date of March 16 for a referendum on the issue.
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