Goals at Kyiv's Olympic National Sports Complex were scored by Junior Moraes (22) and Nabil Fekir (65), Ukrinform reports.
England's Manchester City defeated Germany's Hoffenheim 2-1 in another Group F match.
Manchester City scored 13 points, Lyon eight points, Shakhtar six points, and Hoffenheim three points.
Third-placed Shakhtar will play in the round of 32 of the Europa League next spring.
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