"We will ensure that Gazprom's decision has the least possible impact on European consumers," von der Leyen said.
"Today, the Kremlin failed once again in its attempt to sow division among member states. The era of Russian fossil fuels in Europe is coming to an end."
Gazprom has announced the halt of gas to both Poland and highly dependent Bulgaria after not receiving payment in rubles from the two EU members.
President Vladimir Putin said last month that Russia would no longer accept payments in currencies other than the ruble in retaliation for the West's economic sanctions against Moscow over the war.
Von der Leyen warned EU importers that, unless a supply contract was denominated in rubles, giving in to the Kremlin's demand and paying in rubles would contravene sanctions.
"This would be a breach of the sanctions, so a high risk for the companies," she said.
She said that "about 97 percent" of all EU contracts explicitly stipulate payments in euros or dollars.
Officials said energy ministers from across the bloc will meet on Monday to discuss the situation.
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