Ambassador Gary Koren was called in by the Russian Foreign Ministry for discussions on Friday, Reuters
Israeli aircraft carried out several strikes on Syria last week, prompting the launch of ground-to-air missiles in response - one of which was intercepted.
Russia is likely angered that Israel did not inform Moscow forces about the missile strike beforehand.
Russian troops are also based in the recently won city of Palmyra, aiding pro-regime forces.
On Sunday, an Israeli drone allegedly killed a member of a Hizballah-affiliated group in Syria.
A missile hit Yasser Hussein al-Sayyid's car whilst he was driving on the road connecting Damascus and Khan Arnabeh in the Golan Heights.
The Israeli armed forces refused to comment on the attack and spokespersons for the pro-Assad forces National Defence Forces, of which Sayyid was a member, were not immediately available to give comment on the assassination.