The drones, which can carry explosives, were intercepted on their approach and there were no casualties, according to city mayor Sergei Sobyanin.
The Russian Defence Ministry described it as a “terrorist attack”.
One drone came down in the Domodedovo region south of Moscow and the other fell near the Minsk highway, west of the city.
It is not clear where they were launched from and Ukraine made no immediate comment.
Domodedovo airport is one of Moscow’s busiest.
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The aerial attacks come after flights were halted at Moscow’s Vnukovo airport earlier this month when drones smashed into the city’s business district. They had been jammed by air defences in two incidents.
And in May Russian authorities accused Ukraine of attempting to attack the Kremlin with two drones in an effort to assassinate President Vladimir Putin.
Meanwhile, at least 43 people were injured in a factory explosion north of Moscow today.
Regional governor Andrei Vorobyov said five were feared trapped under rubble at the Zagorsk optical manufacturing plant.
The blast was said to be at a warehouse storing fireworks, which was on the grounds of a factory that makes telescopic sights and other optical equipment for army supplies.
The explosion blew out windows in nearby blocks of flats and prompted the evacuation of the area.
It was unclear what caused the blast.
A thick plume of smoke was also reported billowing over Sevastopol on the Crimean peninsula.
Russia annexed Crimea in 2014. Mikhail Razvozz-hayev, the governor of the port city, said smoke came from a “fleet training exercise” and urged local residents not to worry.
He added: “Yes, the smell is unpleasant but it is absolutely safe. Everything is calm in the city.”
The incidents took place against the backdrop of Ukraine’s ongoing offensive, which officials have warned will be a long slog against the Kremlin’s deeply entrenched forces.
Russia is pushing back in eastern areas, where tough battles are taking place.
Hanna Maliar, Ukraine’s deputy defence minister, said: “In some parts of the frontline multiple changes in position can take place within a day.”
Moscow has claimed that Ukraine has lost tens of thousands of troops but made little progress since the offensive started in June.