Matoukou scored in the Ukrainian side's 3-0 win over ND Mura 05 on 2 August.
But he was ineligible because he had served only half of a two-game ban from 2010 when he was sent off while playing for Genk, also in the Europa League.
Consequently, Uefa's control and disciplinary body have reversed the result in favour of the Slovenian side.
Cameroon international Matoukou was shown a red card in Genk's Europa League qualifier against Porto on 19 August 2010 and he sat out the second leg of the tie.
But having played no further European games for Genk or his next club FC Dnipro Dnipropetrovsk, he had not served the second part of his suspension before taking to the field last week.