The Indomitable Lions advance to the last eight as Group B winners, with DR Congo going through as runners-up.
Yazid Atouba made it 1-0 to Cameroon just before half-time but Jean Makusu equalised straight after the break.
Nicolas Moumi restored Cameroon's lead on 50 minutes and Samuel Nlend sealed the victory with a chipped finish 13 minutes later.
Cameroon will play Ivory Coast in the next round and DR Congo face hosts Rwanda. Both games will be played on Saturday.
Angola beat Ethiopia 2-1 in Monday's other Group B game to record their first points of the tournament as both sides bowed out.
Goals by Papel and Manuel Alfonso gave Angola a 2-0 lead and they saw off a threatened comeback from Ethiopia, who pulled a goal back through Tesfaye, to end their tournament on a high note.
Cameroon beat DR Congo 3-1 to reach the quarter-finals of the African Nations Championship in Rwanda.