The two goals were scored in the first half as the Eagles bounced back from Thursday's defeat.
The Super Eagles are back to winning ways after the shock loss to Central African Republic three days ago in Lagos.
The Eagles soared to a 2-0 win over the Wild Beasts to get their World Cup qualifying quest back on track after the momentary setback suffered in Lagos last Thursday.
Leon Balogun and Victor Osimhen were the goal scorers in a game in which the Super Eagles missed a plethora of chances.
In Sunday's duel played in Douala, the Super Eagles started more fiercely compared to Thursday's outing where they waited for more than 30 minutes before having a clear attempt at goal.
Though far from perfect, the Super Eagles had an improved display in the early exchanges even though the CAR defenders were very physical.
After missing a couple of chances, Balogun broke the deadlock just before the half hour mark.
The Eagles pressed on and just before half time William Troost Ekong provided a cut back for Osimhen in the box and the Napoli striker buried the ball in the net.
The Eagles continued their dominance in the second half and should have increased their lead in the 55th when Osimhen expertly rounded off the goal keeper but his weak shot afterwards was cleared off the line by the CAR defender.
The introduction of Chidera Ejuke for Ahmed Musa in the second half proved to be a smart decision as the Russia-based star cut through the CAR defenders time after time.
Unfortunately, there were no more goals but Super Eagles had done enough for the three points that keeps them firmly on top in Group C.