With some 50 percent of the ballots counted, the referendum results showed than 95 percent of Crimeans backed joining Russia and seceding from Ukraine.
Putin told Obama on the phone that "the peninsulas population was guaranteed free expression of will and self-determination," the Kremlin press service said.
The two leaders agreed to continue seeking ways to resolve the Ukrainian crisis despite the existing contradictions, the press service said.
The political crisis in Ukraine erupted in November following a step back by President Viktor Yanukovych from closer ties with Europe. Months-long protests in the countrys capital Kiev that repeatedly turned deadly eventually led to his ouster by a vote of parliament February 22.
Crimea, along with several other regions in Ukraine, has refused to recognize as legitimate the new leadership in the country.
Obamas press secretary, Jay Carney, said on Sunday that the White House would not recognize the results of the referendum in Crimea describing Russias actions as "dangerous and destabilizing".
Other Western leaders have also denounced the referendum as illegitimate and unconstitutional.
"We dont recognise Crimea referendum or outcome. We call on Russia to enter dialogue with Ukraine and resolve crisis within international law," British Prime Minister David Cameron said in a Twitter post.
President of the European Parliament Martin Schulz said that the referendum violated the Ukrainian and international laws and would complicate further efforts to resolve the crisis.