Officials said the plane twice violated the airspace over the disputed Dokdo/Takeshima islands, which are occupied by South Korea but also claimed by Japan.
South Korea’s ministry of defence said it scrambled fighter jets in response and fired 360 machine-gun rounds.
Russia has denied violating the country’s airspace.
Moscow said two of its bombers carried out a planned drill over “neutral waters” and denied any warning shots were fired by South Korean jets.
But Japan then confirmed its military had also deployed fighter jets in response to the Russian incursion.
Russia later said it had been conducting its first joint long-range air patrol in the region with China, according to Reuters news agency.
This is the first incident of its kind between Russia and South Korea.
What does South Korea say happened?
South Korea’s military said that in total three Russian and two Chinese military aircraft entered the Korea Air Defense Identification Zone (KADIZ) on Tuesday morning.
It said this group was made up of two Russian Tu-95 bombers, one Russian A-50 surveillance plane and two Chinese H-6 bombers.
Russian and Chinese bombers and reconnaissance planes have occasionally entered the zone in recent years.
Overseas aircraft should identify themselves before entering an air defence zone.
South Korea said one of the Russian planes – the A-50 – flew beyond the KADIZ and entered the country’s territorial airspace at around 09:00 local time (00:00 GMT).
South Korean F-15 and F-16 planes were deployed to intercept it.
The military said it fired 10 flares and 80 machine-gun rounds during the alleged first violation.
It said the Russian plane then left before circling back round again, when it was met by 10 more South Korean flares and 280 machine-gun rounds.
In its statement, Russia only mentioned two bomber planes. It did not specifically acknowledge the accusation that it had also sent an A-50 that violated South Korean airspace.
Japan meanwhile has protested against both Russia and South Korea.
Because it claims sovereignty over the islands, Japan’s government said that Russia had violated its airspace. It also said that South Korea’s response was extremely regrettable.