"Humankind has no right to forget the lessons of history and to repeat tragic mistakes," he told participants at the opening ceremony, including Yuri Luzhkov, Mayor of Moscow, and Natan Sharansky, once a Soviet prisoner-of-conscience and now Israel's Minister of Trade and Industry.
"It is bitter to see that our own home-grown fascists have emerged with their racial and national intolerance," Mr Yeltsin said.
My own Jewish friends welcomed the opening of the $10m synagogue. But they were under no illusion that the addition of the Star of David to Moscow's skyline of red stars and Orthodox crosses would solve the deep-rooted anti-Semitism in Russia.
"The Nazis will not change," said Solomon Moiseyev, a retired doctor who supplements his tiny pension by giving guided tours to foreigners. Solomon Moiseyev is not his real name. He is afraid to give that, as recently he has been receiving threats from a petty Russian racketeer, perhaps just wanting to extort money, but probably also motivated by religious hatred.
Anti-Semitism is as strong in Russia today as it was in the rest of Europe before the Second World War - and not only among extreme rightists, who bomb synagogues and desecrate Jewish cemeteries. Because of Soviet propaganda, Russians in general are less aware than other peoples of the extent and horror of the Holocaust. Perfectly pleasant Russian will come out with shocking views on the "Jewish question". As some Bolsheviks were Jewish, many Russians blame all Jews for Communism.
Just as in Western Europe, anti-Semitism became in-grained as the so-called "killers of Christ" were excluded from mainstream society; formed their own tight-knit community, and engaged in business, arousing envy.
In Tsarist times, Jews were not allowed to serve in the army or hold government posts, or to live in Moscow or St Petersburg. So they congregated in cities, like Kharkov and Odessa, becoming financiers, tailors or jewellers.
The Soviet authorities pursued anti-Semitic policies themselves. Even when Stalin stopped purging the Jews and millions of other Soviet citizens, Jewishness was regarded as a nationality to be noted in a person's internal passport and Jews were passed over for the best educational opportunities and jobs.
Dr Moiseyev was able to enter medicine in the 1950s, but only in lowly epidemiology, improving sanitation.
In the 1970s, many Jews, persecuted for acts of faith such as teaching Hebrew, saw Israel as the answer, but ended up in limbo as "refuseniks", denied visas to leave. I remember how Professor Naum Meiman watched his wife, Inna, die of cancer before her exit visa came through.
Not surprisingly, thousands of Jews left at the first opportunity. But others, especially secular Jews, preferred to stay. Dr Moiseyev and his wife "felt we were too old to start a new life all over again".
Those who stayed made grotesque efforts to be accepted. One converted to Russian Orthodoxy, a musicianpoured his energy into Celtic music and became thought of as being of Scottish origin.
Russia may be learning to accept its last one million Jews, but the synagogue-cum-museum has to be locked up and under guard when Russians are revelling nearby, as I found at the weekend.
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