Onuachu put John van den Brom’s men in front with a superb finish after receiving a fine assist from Theo Bongonda in the ninth minute.
Junya Ito doubled Genk’s lead in the 24th minute, firing his effort beyond the reach of goalkeeper Thomas Didillon after he was set up by Bryan Heynen.
The action-packed first-half also saw Hannes van der Bruggen receiving a red card in the 39th minute, having previously been cautioned earlier in the game, to leave Cercle Brugge with one man short.
Both sides failed to find the back of the net in the second half as the Green and Black frustrated every effort from the Luminus Arena outfit to try and increase their lead, despite their numerical disadvantage.