The visitors got the curtain raiser through Sami Kahli in the 11th minute and had their advantage doubled before the half-hour mark as Raphael Lecomte effort found its way past Hendrik van Crombrugge.
Eight minutes after restart, Onyekuru started the comeback for the hosts after he scored the first of his brace.
The 19-year-old got his second and his side's equaliser in the 76th minute to save Jordi Condom’s men from an embarrassing home defeat at the hands of the Belgian First Division B outfit.
The goals saw the winger lead the playoff’s goalscorers' ranking with two goals from an encounter.
And his side are placed fourth in the Group B of the playoff table as Gent and Kortrijk occupy the first and second spots respectively, with three points apiece. Roeselare are third leveled on the same point with the Pandas.The second round of playoffs fixtures sees Eupen travel to fifth-placed Royal Excel Mouscron on April 8 as they continue in their bid to qualify for the European second-tier competition.