Friday's attack was the second such raid in barely a week against US billionnaire George Soros' charity's headquarters, police said.
The guards were rushed to hospital, Interfax reported, adding it was not immediately clear whether the assailants had succeeded in invading the building.
Last week, 50 paramilitary men seized the Foundation's Moscow offices and confiscated its computer records and archives, paralysing its work.
The raid was ordered by the building's owner, ostensibly because of a long-standing dispute over rent.
But the head of Soros's Open Society Institute in Russia, Yekaterina Geniyeva, said the operation appeared to have political motives.
1930 - Born in Hungary
1952- Graduates from London School of Economics
1956- Moves to USA
1987 - Sets up Soros Foundation-Soviet Union
1992 - Helps bring down the sterling
1997 - Accused of trying to wreck Malaysia's economy
The action came just days after Soros publicly criticised the jailing of Russian oil tycoon Mikhail Khodorkovsky as "persecution" that would force business to submit to the state.
Khodorkovsky, former boss of the Yukos oil giant, has been in jail since 25 October on seven charges ranging from fraud and tax evasion to embezzlement.
The campaign against Yukos is seen as a Kremlin warning to big business to stay out of politics, and a bid to restore state control over the nation's energy resources.
The Soros Foundation is heavily involved in promoting civil society and the development of democratic ideas, chiefly in former Soviet bloc countries.
But Hungarian-born Soros, who has long had difficult relations with Moscow, announced in June that he was sharply curtailing his philanthropic activities in Russia.
He is widely known as the man who broke the British pound in 1992, after helping force sterling out of Europe's exchange rate mechanism.
Soros was also reportedly the first American to earn a billion dollars in a single year.