It was the first time Iranian naval ships have used the canal since Iran's 1979 Islamic revolution. The French news agency reported on Wednesday that NATO was monitoring their movement.
Israeli President Shimon Peres told a conference in Madrid Wednesday that the passage of the two Iranian ships into the Mediterranean was more of a "provocation" than a threat to Israel.
Peres said Israel faces a greater threat from Iran's nuclear program. Israel and Western nations suspect Iran is trying to build nuclear weapons - a claim Tehran denies.
Israeli Prime Minister Benjamin Netanyahu criticized the naval movement as a ploy by Iran to expand its regional influence at a time of instability.
The international Convention of Constantinople, signed in 1888, guarantees the right of passage through the Suez Canal for all seagoing vessels - military or civilian.