Rabiu Ali netted a brace and the other goals came through Ede Ifeanyi and substitute Barnabas Imenger, while Dario Khan and Diogo were on target for Mozambique.
The Mambas opened the scoring in spectacular fashion in the 10th minute when Khan beat Chigozie Agbim with a dipping free kick from just outside the centre circle.
The Super Eagles replied just a minute later as Mozambique failed to clear the lines from a throw-in, allowing an unmarked Ede to finish from the edge of the six-yard box.
Stephen Keshi’s side stormed to the lead in the 13th minute as Ali took advantage of a defensive error to beat Soarito with a powerful strike from just outside the box.
Manuelito had a golden opportunity to level matters at the other end two minutes later when he was put through on goal, but his shot was blocked by the onrushing Agbim.
The Nigeria goalkeeper should have done better in the 20th minute when he came out to cut a through-pass from Maninho, but he failed to get to the ball, leaving Diogo with the easy task of passing the ball into an empty net.
The two sides adopted a more cautious approach during the second part of the first half and eventually went into the break with the scores level at 2-2.
Nigeria started the second half brightly and in the 54th minute they were awarded a penalty as Mozambique captain, Khan, was adjudged to have handled the ball inside the penalty area.
Ali stepped up to take the kick and made no mistake as he sent Soarito the wrong way to score his second goal of the match.
The Mambas pushed forward for the equaliser but Josimar fired wide from long range in the 61st minute, while Maninho also missed the target at the near post in the 74th minute.
Then it was Nigeria who came close to extending their lead in the 75th minute, but Salami saw his shot cleared before the line by Miro, while Abdullahi Shehu shot straight at Soarito.
Joao Chissano’s side came close at the other end in the 83rd minute when Miro delivered a powerful free kick across goal but Khan arrived a second too late at the far post.
The Super Eagles sealed the win in the 88th minute when Imenger ran onto a through-pass from Kwambe Solomon before chipping the ball over the onrushing Soarito and into the back of the net.