The goals at the Metalist Stadium in Kharkiv were scored by Bernard (26), Ismaily (32), and Kun Aguero (90+2, penalty).
The match was handed by a team of French referees headed by Benoit Bastien.
In another Group F fixture, Feyenoord beat Italy's Napoli 2-1 in Rotterdam.
Standings: Manchester City - 15, Shakhtar - 12, Napoli - 6, Feyenoord - 3.
Thus, Shakhtar finished second in their group and will play next spring in the last 16 of the most prestigious European football tournament.