The two men talked hours after Russia's upper house of Parliament approved Putin's request for the country to take military action in Ukraine.
Putin said he made the request in order to protect the lives of ethnic Russians living in the Ukrainian peninsula of Crimea, RIA Novosti reported. About 60 percent of Crimea is made up of ethnic Russians.
All 90 Senators present in the 116-member Federation Council voted to authorize use of armed force in Ukraine and the Kremlin said the troops will remain there until the "political-social situation in the country is normalized."
Russia's Black Sea Fleet is based in Crimea.
The White House, in a readout of the phone conversation between the presidents Saturday afternoon, said Obama expressed "deep concern over Russia's clear violation of Ukrainian sovereignty and territorial integrity" citing Russia's obligations under the U.N. Charter, the 1994 Budapest Memorandum and the Helsinki Final Act.
"The United States condemns Russia's military intervention into Ukrainian territory," the White House said.
Putin told Obama that Russian-speaking ethnic groups in Crimea and elsewhere in Ukraine were being attacked by "ultranationalists" supported by the acting Ukrainian leadership.
The United States suspended participation in scheduled meetings to prepare for a G-8 summit in Russia.
At the United Nations, the 15-member Security Council met in urgent session for the second day as Secretary-General Ban Ki-moon called for direct negotiations to defuse the growing tensions in the Crimea region. Ban also planned to talk directly to Putin, the UN News Centre said.
"The Secretary-General reiterates his call for the full respect for and preservation of the independence, sovereignty and territorial integrity of Ukraine," Ban's spokesman said in a statement.
On Thursday, Crimean Premier Sergey Aksyonov, who took office after armed men took over the Crimean parliament building, asked Putin for help in deterring anti-government protesters, CNN reported.
Aksyonov told the Russian state channel Russia 24 that Ukrainian security forces currently "are unable to efficiently control the situation in the republic."
"I am appealing to Russian President Vladimir Putin to provide assistance in ensuring peace and accord on the territory of the Autonomous Republic of Crimea," he said.
Earlier Saturday, members of Russia's upper and lower houses of parliament called on Putin to act on the situation in Crimea, Russia's state-supported RIA Novosti news agency reported. The measure authorizing use of armed forces only required passage in the Federal Council, the upper chamber.
In a televised address Saturday, acting Ukrainian President Olexander Turchynov said he has ordered the army on full alert but urged Ukrainians to not be provoked by Russia's actions.
Scuffles, some bloody, erupted between pro- and anti-Moscow protesters during rallies in the cities of Donetsk, Kharkiv and Mariupol, the BBC reported
Ukrainian interim Prime Minister Arseniy Yatsenyuk accused Russia of recently deploying 6,000 extra soldiers to Ukraine to cause a provocation, the BBC said.
The presence of Russian soldiers is a provocation and we demand that Russian soldiers return to their permanent bases," Yatsenyuk said. "We are taking no steps that could provoke a violent confrontation. All responsibility for the escalation of the conflict lies personally at the leadership of the Russian Federation."
When asked about why Russian troops were deployed to the Crimea, Russia's U.N. envoy Vitaly Churkin said Moscow's actions in Crimea were in line with Black Sea Fleet agreement, ITAR-Tass reported.
"We have an agreement with Ukraine on the presence of Russia's Black Sea Fleet in Sevastopol, and we have been acting within the framework of those agreements," Churkin said after a discussion of the Ukrainian issue in the U.N. Security Council Friday.
The agreement between Moscow and Kiev was signed by leaders of the two countries on April 21, 2010.