Mousavi was appointed in August as the commander of the Iranian army, an entity separate from the country's Revolutionary Guard corps.
Speaking at an event in the holy city of Qom, he elaborated on the remarks he made last month about Israel not surviving 25 years, explaining that he never meant to say the regime would necessarily last that long.
"That we say that the Zionist regime will not see 25 years later doesn't mean that it will certainly survive for 25 years," he said according to the semi-official Fars News Agency.
"There is a prerequisite for this famous sentence, that is if the Zionist regime makes any wrong move, Haifa and Tel Aviv will be razed down to the ground."
Key points of the historic nuclear deal include a "long-term" International Atomic Energy Agency (IAEA) presence in Iran that includes the monitoring of uranium ore concentrate produced by Iran for 25 years.
"You will not see next 25 years (…) With God's grace, nothing under the name of the Zionist regime will exist in the region by then," Khamenei said on Twitter.
On Monday, US President Donald Trump warned that Washington will walk away from the deal if it concludes that IAEA is not tough enough in monitoring it. Iranian nuclear chief Ali Akbar Salehi responded that the greatest threat to its survival was "the American administration's hostile attitude."