Speaking at the Institute for National Security Studies' conference in Tel Aviv, Ya'alon said Iran poses a greater threat than Daesh, and that if Syria fell, Israel would prefer that Daesh was in control of the territory rather than an Iranian proxy.
"In Syria, if the choice is between Iran and [Daesh], I choose [Daesh]. They don't have the capabilities that Iran has," Ya'alon said, according to the Times of Israel.
Ya'alon reasoned that Iran had greater capabilities than Daesh and remained the biggest threat for Israel.
"We believe [Daesh] will be eventually defeated territorially after the blows it has been suffering, and in light of the attacks on its oil reserves," he told the conference, according to Ynetnews.
"Our principal enemy is Iran, after I heard people here say here other things," Ya'alon said, likely alluding to comments by IDF Chief of Staff Gadi Eizenkot, who on Monday told the same forum that Hezbollah is the most serious threat to Israel.
Ya'alon warned that, with the lifting of the sanctions, Iran will now be able to sign arms deals worth tens of billions of dollars that will further finance its proxies in the region.
He said that "Iran's terror infrastructure exists today on five continents: Asia, Africa, Europe, South and North America."
The United States and European nations lifted some sanctions on Iran on Saturday after international inspectors concluded that Tehran had followed through on promises to curb its nuclear program.
Ya'alon and Israeli Prime Minister Benjamin Netanyahu have spoken out publicly against the US-backed nuclear deal with Iran.
"There's a camp that would like to rely on America's lead and is sometimes greatly disappointed because the Americans view Iran as a partner," Ya'alon said of US-Israel ties.