Pillay said the events during fighting for control of the town of Khan al-Assal in the northern province of Aleppo were "deeply shocking".
Video footage shot by rebels and information provided by the Syrian Observatory for Human Rights suggest dozens of members of regime forces were executed.
"There needs to be a thorough independent investigation to establish whether war crimes have been committed. And those responsible for such crimes should be brought to justice," Pillay said.
She added that the material gathered by her office suggested the overall toll in the Khan al-Assal battle was much higher.
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The world's attention has focused mainly on massacres committed by President Bashar al-Assad's regime since a popular uprising broke out against his rule in March 2011.
The protests soon evolved into a fully-fledged civil conflict, with jihadist foreign fighters taking a leading role in the rebellion, and Pillay warned the latest executions were evidence that abuses were being committed on both sides.