The move appeared calibrated to avoid pushing the Mideast closer to all-out war between two of its strongest military powers, with no casualties immediately reported.
Combat pitting the Jewish state against Iran-backed Lebanese Hezbollah and Palestinian Hamas has ratcheted up in recent weeks, bringing Iran and Israel into more direct confrontation.
Multiple explosions were heard in and around Tehran at around 2:15 am local time and several hours later again in the capital and in two southwestern cities.
The Israeli military said "The retaliatory strike has been completed and the mission was fulfilled," adding that "aircraft struck missile manufacturing facilities used to produce the missiles that Iran fired at the State of Israel over the last year."
Targets also included surface-to-air missile and anti-aircraft capabilities, the military added.
“Iran reserves the right to respond to all attacks and there’s no doubt that Israel will get a proportionate response to any action” IRGC-affiliated Tasnim news agency quoted an informed source as saying.
They added that "initial assessment shows the Zionist regime’s actions were weak.”
The United States, Israel's main political and military backer, described the attack on their mutual archenemy in the region as self-defense.