Onuachu opened the scoring in the 17th minute of the encounter with a fine finish after receiving a timely assist from Daniel Munoz.
The 26-year-old centre-forward came close to double his side’s lead in the 34th minute but his strike missed the target.
Matt Miazga then turned the ball into his own net moments before the hour mark to help John van den Brom’s men increase their lead.
Genk were reduced to 10 men in the 71st minute after Jhon Lucumi was shown a straight red card for serious foul play and Anderlecht capitalized on their numerical advantage to reduce the deficit through Adrien Trebel.