He did not name the airliner that was flying from Tehran to Damascus, but information from flight tracker Flight Radar indicated it was likely a Syrian Cham Wings aircraft.
On Thursday, Israeli warplanes launched airstrikes at targets in southern Syria, according to Syrian state media. Konashenkov said the incident followed airstrikes by four Israeli F-16 fighter jets.
The incident comes a month after Iran shot down a Ukrainian passenger jet shortly after takeoff from Tehran, killing all 176 passengers and crew.
The Ukrainian jet was hit by an air defense battery of the Islamic Revolutionary Guard Corps in the tense hours after Iran carried out retaliatory missile strikes against U.S. positions in Iraq after the United States killed a senior Iranian commander, Qasem Soleimani, in Baghdad.
According to Konashenkov, Israeli fighter jets fired eight missiles at targets near Damascus early Thursday, and Syrian forces fired antiaircraft missile defense systems.
"It was purely thanks to the prompt actions of air traffic controllers at Damascus airport and the effective operation of the automated air traffic control system that the Airbus 320 passenger plane was promptly rerouted from the Syrian air defense area of engagement and safely landed at the nearest reserve airfield - the Russian air base Hmeimim," he said.
Konashenkov said the use of civilian aircraft as shields to deter Syrian forces from responding to attacks was "becoming a signature feature of the Israeli air force." He added: "Unfortunately, such operations of Israeli strategists do not care in the slightest about the lives of hundreds of absolutely innocent civilians."
In September 2018, Russia blamed Israel when Syrian forces shot down a Russian military plane while they were responding to an Israeli strike. Israel said Syria bore full responsibility for the incident.
The 2018 incident caused a spike in Russian-Israeli tensions over Syria and prompted Russia to deploy its own S-300 surface-to-air missiles in Syria to bolster its defenses.
However, after Israeli Prime Minister Benjamin Netanyahu called Russian President Vladimir Putin to express his sorrow over the incident, Putin described it as "a chain of tragic accidental circumstances."
Israel does not normally comment on its actions in Syria, but the Israel Defense Forces have confirmed recently that they have launched attacks in Syria to prevent Iran from entrenching there.
Konashenkov said the passenger flight should have been clearly visible to Israeli radar.
The Syrian Observatory for Human Rights, a monitoring group based in Britain, said airstrikes Thursday hit the positions of Iranian-backed militias, killing 23 people, including Syrian and Iranian fighters.
In recent weeks, Syrian forces backed by Russian airstrikes and fighters supported by Iran have mounted attacks in the northwest of the country in a bid to crush the last stronghold of opposition to Syrian President Bashar al-Assad.