After a 1-0 victory against Angola and a goalless draw with Ethiopia, the Indomitable Lions knew they needed a win to secure their place in the last eight.
Barely a minute after the start, Nlend missed the target from close range and Ngamaleu parried the ball from outside the box and it went over the line.
Despite dominating, Cameroon had to wait until the 40th minute when Yazid Atouba broke the deadlock when he connected perfectly with an Ngamaleu cross from the left.
Striker Makusu Mundele levelled for DR Congo two minutes into the second half but Ngamaleu regained the lead for Cameroon with a thunderous volley in the 52 minute before Nlend added the third goal when he clipped the ball over the advancing Congolese keeper in the 64th.
DR Congo then made a tactical change by replacing Guy Lisadisu with fellow midfielder Heritier Luvumbu to try and contain the Cameroonians in the midfield but it made no difference as the Congolese coach Florent Ibenge was left rueing his decision to make nine changes to the team that beat Angola 4-2 in the second match.
Angola beat Ethiopia 2-1 at the Amahoro stadium in a match that had no bearing on the results from Group B, as the two teams were already out of the running.
Cameroon topped the group with seven points and will play the Ivory Coast while second-placed DR Congo will take on the hosts, Rwanda in the quarter-finals.
Both matches will be played on Saturday at the Stade Huye and at the Amahoro National stadium in Kigali respectively.