During the conversation, Merkel expressed "concern about the situation in eastern Ukraine", her spokesman Steffen Seibert said in a statement.
"In order to establish a ceasefire as quickly as possible, the chancellor asked the Russian president to help calm the situation," the statement said.
Merkel also "expressed hope that the humanitarian convoys reach their destination quickly, to relieve the suffering" in Ukraine.
Kiev and Moscow have been wrangling for days over a Russian convoy that Moscow says is carrying humanitarian aid for besieged rebel-held cities but which Kiev suspects could be a "Trojan horse" to provide military help to the insurgents.
The call comes ahead of a planned summit in Berlin on Sunday that will be attended by foreign ministers from France, Russia, Ukraine and Germany, Seibert said.
It follows a tense day marked by reports of a Russian military incursion into Ukraine, which was immediately denied by Moscow.
Merkel, a fluent Russian speaker, has held regular talks by telephone with Putin, who served as a KGB agent in Dresden during the Cold War, since the Ukraine crisis erupted, urging respect for Ukrainian sovereignty.