"The Israeli aggression targeted some positions in Sheikh Najjar industrial zone and a number of enemy missiles were brought down," an army statement said.
The state-run Syrian news agency Sana said that the country's air defenses were "in operation" over Aleppo and claimed that they had brought down 70 percent of their targets.
The strike reportedly took place while the United Nations Security Council was discussing the US recognition over Israeli sovereignty over the Golan Heights.
There was no immediate comment from Israel.
The blasts caused an electrical blackout in Aleppo, the country's second largest city and a major industrial hub that bore the brunt of years of fighting and heavy Russian and Syrian aerial bombardment on its former rebel-held areas.
Military experts say Aleppo is one of the main areas where Iran's elite Revolutionary Guards have a strong military presence supporting local militias that have for years been fighting alongside the Syrian army to defeat insurgents.
Two opposition sources familiar with Tehran's military presence in the area said large ammunitions depot and a logistics hub that belonged to Iranian-backed militias inside the industrial zone received direct hits.
Other strikes hit the vicinity of Nairab military airport on the outskirts of Aleppo in the second such strike on the installation used by Iranian troops in less than a year, they added.
Iranian-backed Shiite militias have expanded their control over mainly Sunni areas around Damascus, southern and eastern Syria that bore the brunt of the heaviest bombardment and led to mass displacement or emigration to neighbouring countries.
Iran's growing influence in Syria, where it has struck economic and trade deals, has raised the prospect of a military confrontation with Israel.
Israel, which considers Iran its biggest threat, has repeatedly attacked Iranian targets in Syria and those of allied militia, including Lebanon's Hezbollah.
Earlier this year the IDF said they had attacked Iranian targets that included munitions stores in Damascus International Airport.
Prime Minister Benjamin Netanyahu has said Israel had carried out "hundreds" of attacks over the past few years of Syria's war to curtail Iran and its ally Hezbollah.
Israel has said it was crucial to block growing Iranian military influence in Syria and has vowed it would push its troops out of the country.
Iran has warned Israel it would respond if it continued attacking targets in Syria and repeatedly said its military presence in Syria is at the invitation of the Assad government and it has no immediate plans to withdraw.