In a statement announcing the unusual meeting also attended by Germany's Foreign Minister Heiko Maas, Merkel's spokeswoman Ulrike Demmer said the talks were arranged by Merkel and Russian President Vladimir Putin last week.
“The focus of the talks was the situation in the Near East, in particular in Syria. The conflict in eastern Ukraine was also discussed,” added Demmer.
Separately, the Russian foreign ministry confirmed the meeting, saying the parties discussed the situation in Syria.
These included “tasks related to the preparation of conditions for the return of refugees and the advancement of the political process,” said Moscow, which backs Syrian President Bashar al-Assad in the conflict.
The meeting also discussed “ongoing work within the 'Normandy format' to fulfil the Minsk agreements” and several bilateral issues, the ministry said, referring to the 2015 Ukraine peace plan brokered by France and Germany in the Belarussian capital.
After a Western-backed popular uprising in Kiev in 2014 ousted a pro-Kremlin government, Russia annexed the peninsula of Crimea and supported a separatist insurgency in Ukraine's Russian-speaking eastern regions of Donetsk and Lugansk.
The Ukraine conflict has claimed over 10,000 lives.
Despite repeated ceasefire deals, the Minsk agreements are violated on a near daily basis, with clashes between pro-Russian and Ukrainian forces.
During a summit between Putin and US President Donald Trump last week, the Kremlin chief reportedly suggested that a referendum be held in eastern Ukraine.
Moscow has also put forward plans to Washington to cooperate on the safe return of refugees to Syria.