China's Gong Jinjie and Guo Shuang twice set the world record, in qualifying and in the first round, and finished first in the final in 32.619.
However, officials ruled the takeover between the pair was illegal and Germany, who clocked 32.798, were promoted to gold.
Australia's Anna Meares and Kaarle McCulloch put in 32.727 and claimed bronze ahead of Ukraine.
It was the second relegation of the event after Great Britain's Jess Varnish and Victoria Pendleton were penalised for a takeover infringement. They had set the second fastest time in the first round.
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