A spokesman for the US-led coalition battling the Islamic State group said it was not responsible for the strikes.
Observatory head Rami Abdul Rahman said it was "likely" that Israel mounted the operation, which killed several Iraqi as well as Iranian fighters.
State media did not report the strikes.
Iranian-backed militias and their allies command a significant presence in eastern Syria south of the Euphrates Valley. The region lies close to the Iraqi border.
Israel has launched hundreds of strikes in Syria since the start of the civil war in 2011, targeting government troops, allied Iranian forces and Hezbollah fighters.