Vladyslav Kulach scored the only goal in the 48th minute.
In another Group E match, Portugal's Sporting lost 0-1 to England's Arsenal in Lisbon.
Arsenal collected nine points after three games, followed by Sporting (six points), Vorskla (three points), and Qarabag (zero points).
In the fourth round of the Europa League on November 8, Vorskla will play Qarabag in Poltava, and Arsenal will face Sporting in London.
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