The call took place amid accelerating international diplomacy hours before a ceasefire deadline set by Kofi Annan for an end to 13 months of operations against Syrian rebels by President Bashar al-Assad's forces, which have killed thousands of people.
"The President and Chancellor shared the concern that the Assad government was not complying with the terms of the agreement negotiated by Kofi Annan and continued to engage in unacceptable brutality against its own people," a White House statement said.
"They agreed that this underscored the need for the UN Security Council to come together to take more resolute action."
Syria earlier announced that it would cease military operations against rebel fighters from Thursday.
UN envoy Annan said he had received a written pledge from Damascus that regime forces would halt their operations from dawn, provided they did not come under attack.
But the opposition and foreign governments said there was no sign of compliance on the ground by the regime as its forces continued to pounded protest centers, killing 14 civilians on Wednesday, according to monitors.
Obama and Merkel also expressed hoped that Iran would take advantage of talks in Turkey with world powers Britain, China, France, Germany, Russia and the United States which start on Saturday to address concerns about its nuclear program.
"They also reiterated their common resolve to increase the pressure on the Iranian regime through sanctions and other measures if it remained unresponsive," the White House statement said.