German Foreign Minister Frank-Walter Steinmeier said the elections went "against the letter and spirit" of an internationally brokered truce deal in September that was meant to halt the war in eastern Ukraine.
Steinmeier urged Russia to respect "the unity of Ukraine."
"We will judge Russia and President (Vladimir) Putin on their statements that the unity of Ukraine cannot be called into question," he said on Twitter.
Earlier, EU foreign affairs head Federica Mogherini issued a statement slamming the rebel leadership elections as "a new obstacle on the path towards peace in Ukraine."
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Russia, which risks facing a ratcheting up of already punishing EU and US sanctions, ignored Western appeals ahead of the vote and gave its full backing to elections that the Ukrainian government branded an illegal "farce."
"We respect the expression of the will of the residents of southeast (Ukraine)," the Russian foreign ministry said in a statement on Russian news agencies.
Separatist leaders in eastern Ukraine described the polls as a step toward formalising their de facto independence from Ukraine after seven months of fighting in which the United Nations says more than 4,000 people have died.
The separatist uprisings in a corner of Ukraine with long-held pro-Russian and pro-communist leanings started shortly after Russian troops invaded and annexed Crimea, a southern Ukrainian region, in March.
Russia justified that dramatic seizure of its neighbour's territory by saying it needed to protect ethnic Russians from a surge of Ukrainian nationalism during the previous month's pro-Western revolution in the capital Kiev.