Attisso Kodjo scored the decisive goal just before half-time, giving the Rwandan side a lead they held on to until the final whistle.
Rayon Sports now sit second in Group C with six points, level with Al Hilal of Sudan but behind them on goal difference. Al Hilal have scored six goals compared to Rayon Sports’ three.
The result keeps Rayon Sports firmly on course for a place in the knockout stages after another disciplined display at the Kigali Pele Stadium.