They spoke following Monday's deadly bomb attack on a metro train in Russia's second-largest city of St. Petersburg which killed 14 people and wounded 50.
The Kremlin said the leaders also discussed the situation in Ukraine and the Easter ceasefire declared from April 1, Reuters reported.
A German government source said: "Merkel urged Putin to use his influence with the separatists (to keep to the April 1 ceasefire)."
The Kremlin added that Putin, Merkel and Hollande have agreed to continue contacts on Ukraine.