Footage on social media showed blue paint splashed across the icon, which Georgian media said has been displayed in Tbilisi's Holy Trinity Cathedral for several months.
As authorities began investigating, the case exposed deep fractures in Georgia over Stalin's legacy in his homeland.
Stalin's supporters - in Russia as well as in Georgia - hail him as the man who defeated Nazism in World War Two.
"He was a big, big person. On this, I cant even express myself as an ordinary person. Stalin was a god-send and we need one like that."
But his critics see a bloodthirsty dictator who sent millions to the Gulag labor camps and presided over the Great Terror of 1936-38 in which historians say up to 1.2 million people died.
That sentiment was also evident on the streets of Tbilisi.
"I feel very insulted after what I saw at the church, I think it's an insult for the Georgian society to have Stalin's icon at the church, because Stalin brought many bad things to the people, ruined people's lives and there is no place for him there."
Stalin was born Josef Dzugashvili in 1878 in the Georgian town of Gori.
There, a museum commemorating his life and work continues to attract a steady stream of tourists, though his statue in the town square was removed in 2010.
After consolidating his power following the death in 1924 of Bolshevik leader Vladimir Lenin, Stalin ruled the Soviet Union with an iron hand until his death in 1953.
Stalin was an avowed atheist who violently repressed religion across the Soviet Union, though the icon shows him being blessed by St. Matrona of Moscow, a Russian Orthodox saint, during World War Two.
A Georgian nationalist party called the Alliance of Patriots, which has also expressed pro-Russian views, said it had gifted the icon to the cathedral.
The icon has since been cleaned and the cathedral placed under police guard.
