Elohim Rolland got the opener for the visitors in the 16th minutes before Jeffren Suarez levelled the tie two minutes after the half-hour mark.
Moments before halftime, Onyekuru gave his side the lead, for the first time in the game, after he converted past Thomas Kaminski from the spot.
The 19-year-old winger then proceeded to secure the maximum points for the Pandas with his second of the game in the 80th minute.
The Guys threatened a comeback with an Andriy Totovitskiy goal from the spot but Jordi Condom’s men stood firm for the win.
Onyekuru who is subject of several transfer speculation across Europe has now scored eight goals in eight Europa League playoff encounters. And has taken his season’s tally to 22.
The win sees his team move to third spot in the log after garnering ten points from eight games.
On Wednesday, the Kehrwegstadion outfit will face Royal Excel Mouscron in their next playoff encounter in a bid to qualify for Europe’s second-tier club competition.