The strikes reportedly targeted militant ISIS "shelters" east of the ancient city, which housed heavy equipment and militant troops transferred from ISIS' de facto capital Raqqa.
"The Admiral Essen frigate and Krasnodar submarine of the Russian Navy conducted strikes by four Kalibr cruise missiles on objects of the ISIS terrorist grouping near Palmyra from the eastern part of the Mediterranean Sea," the Ministry statement said. "All targets have been hit."
The statement said the strike "confirmed the high combat readiness of the Russian Navy forces," and noted that the US, Turkey and Israel were informed of the strikes at the "appropriate time."
"(The US, Turkey and Russia) all have the same stated position of destroying ISIS, and so they cooperate on some level," says CNN's Matthew Chance.
"All sides are in direct contact with each other and all go to some effort to coordinate their strikes on ISIS and other targets."
The Kalibr missiles are the newly-developed Russian equivalent of the US' Tomahawk missile, but cost a fraction of the price, says Chance.
"They're new but it isn't the first time they've used these missiles -- last year they were (fired) from a flotilla in Caspian Sea.
"(Syria) is an important platform. Russia is testing its newly developed weaponry in the Syrian war zone -- it uses Syria as test bed, then takes orders from potential buyers -- the Russian government is one of the world's biggest arms exporters."
The strike takes on significance given that Russia doesn't often strike ISIS targets, instead usually focusing efforts on the Syrian government's foes, Chance says.
A UNESCO World Heritage Site, Palmyra is home to globally important archaeological ruins and is seen as a symbolically important to both sides.
"Russia promotes its activity against ISIS in Palmyra as fighting on behalf of western civilization and (this attack) shows Russian (anti-ISIS) efforts in a good light," Chance says.
Its cultural significance means that it acts as a propaganda win for the Russian forces. After first retaking the town in May 2016, Russian forces held a concert in the city's ancient amphitheater
However, criticism has been leveled that "efforts to retake Palmyra are merely window dressing, that it is more significant culturally than militarily," Chance says.
The city does have some strategic value, says CNN's Tim Lister; there are oil pipelines and refineries in the area, as well as phosphate mines.
"It is also the only way the regime can reconnect (on the ground) with its isolated and besieged outposts in Deir Ezzour," he says.
Control changes hands
Control of Palmyra has passed from the regime to ISIS and back again a number of times since the militant group first captured it in 2015.
In March, Syrian forces, backed by Russian aircraft, took back the city
from ISIS militants. At least 1,000 ISIS militants were killed or wounded in the offensive, according to the Russian Ministry of Defense.
ISIS is still active to the east and north-east of the city, as well as in a few patches south of the city, where airstrikes against an ISIS convoy occurred at the weekend, Lister says.
Located in Homs province, in central Syria, Palmyra is around 225 kilometers (140 miles) from Raqqa, considered ISIS' headquarters in Syria.