The Fordow Fuel Enrichment Plant has enriched a huge amount of uranium to the 60% level, has tremendous enrichment capacity, and is based in Qom Province.
Multiple Iranian weapons and missile launchers were destroyed in the air force strikes.
The strike killed the head of the Revolutionary Guards' intelligence organization and his deputy, as well as the head of the Quds Force's intelligence branch and his deputy.
In the coming hours, Israel is expected to order residents of various neighborhoods in Tehran to evacuate, followed by strikes on infrastructure and government buildings.
The execution is the third in recent weeks related to the conducting of espionage on behalf of Israel.
Israel's Air Force and Navy intercepted over 100 drones fired by Iran so far, with no reports of any that fell in Israeli territory, the military added.
The identity of the two suspects, as well as further details into the investigation, are under an active gag order.
Israel had prepared for the possibility that the war could last for weeks, but that timeline may now be shortened.
Meanwhile, Trump wrote on social media that Israel and Iran should and will make a deal soon and called to make the Middle East great again.
Israelis on social media reported hearing explosions, particularly in the Tel Aviv and Haifa areas.