Goals were scored by David Silva (30), Aymeric Laporte (35) and Bernard Silva (71), Ukrinform reports.
Another Group F match between Germany's Hoffenheim and France's Lyon ended in a 3-3 draw.
Manchester City tops the group with six points, followed by Lyon (five points), Hoffenheim (two points), and Shakhtar (two points).
In the fourth round, Shakhtar will play Manchester City in England, and Lyon will take on Hoffenheim at home. The matches will take place on November 7.
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