The Super Eagles finished their second round qualifying group with a maximum 18 points from six matches while Sierra Leone finished with seven points.
Nigeria have now qualified for the draw for the third round of the qualifying tournament, which also serves for the 2010 Africa Cup of Nations in Angola, which will be staged in Zurich on 22 October.
The home team opened scoring in the 19th minute through midfielder Christian Obodo when he slotted home after a goalmouth scramble.
However, Sierra Leone were level after 33 minutes when an misunderstanding between central defenders Joseph Yobo and John Shittu saw Yobo conceded an own-goal.
Nigeria restored their lead two minutes later when Beijing Olympics star Victor Obinna netted his team's second goal before Osaze Odemwingie increased the Eagles advantage with another fine effort in first half stoppage time.
Russia-based defender Chidi Odiah scored the best goal of the day when his clean strike from outside the box beat the Sierra Leonian goalkeeper.