Here's a helpful map visualizing how Russia and Germany divided Eastern Europe in the secret protocol[1] to the Hitler-Stalin pact:
https://i.imgur.com/DvCrPWB.jpegAs to the "Judenfrei" status, that's a great deal due to the executions and mass deportations[2] that Russians unleashed after invading in 1940. First they banned all Jewish organizations, even fraternities and tennis clubs. Then they started targeting the professional class (politicians, doctors, lawyers, etc) to wipe out people capable of running the country and challenge the Russian rule. Their crime was officially designated as "being socially undesirable". Jews were overrepresented among the victims by a factor of 10. By the time Germans arrived in 1941, only 900 Jews were left in Estonia, as depicted on your map. Some had been deported, others ran away wherever they could. The last 900 remained because they believed that Germans couldn't be worse than the Russian terror of 1940-1941.
When Russians invaded again in 1944 and began their 50-year occupation of the country (which included another wave of terror and mass deportations[3]), they replaced German antisemitic policies with their own and continued suppressing Jewish culture until the very end of the USSR. The Jewish school in Tallinn, for example, opened in 1924, was closed by Germans in 1941, and only in 1990, as the USSR entered the final death spiral, got its confiscated real estate back and resumed teaching. So if you intended to be clever and play the Jewish card, you chose a very wrong place to do it. Germans had the holocaust in store for them, and for Russians they were exploiters of the working class, destined for Siberian labor camps.
[1] https://en.wikipedia.org/wiki/Molotov%E2%80%93Ribbentrop_Pac...
[2] https://en.wikipedia.org/wiki/June_deportation
[3] https://en.wikipedia.org/wiki/Operation_Priboi