South Africa's goalless draw against Seychelles earlier on Tuesday had opened up the chance for the Super Eagles to move into a commanding position in the log and Ighalo's clinical showing helped the west Africans' hold off a much improved Meditteranean Knights side.
The visitors scored two quick-fire goals via the former Watford attacker and stand-in captain, Musa before the Omar Al-Maryami's charges fought back through Mohamed Zubya and Ahmad Benali.
Ighalo's goal nine minutes from time ensured the Super Eagles continue their 100 percent record since after their below-par World Cup campaign in the summer.
Gernot Rohr stuck with the side that did the job in Uyo four days ago, with Ola Aina starting in place of the injured Shehu Abdullahi. His opposite number Al-Maryami opted to provide support for tormentor-in-chief Mohamed Anis Saltou in his attack, with Zubya introduced.
Ighalo got the Super Eagles started on the right foot opening the scoring in the 13th minute after benefitting from a good Musa-Iwobi exchange, with the former providing the assist for the striker's fifth goal in the qualifying campaign.
Moments later, the Changchun Yatai marksman returned the favour, releasing Musa who scrambled home the visitors’ second of the evening.
The momentum soon shifted to the Libyans who tested Francis Uzoho a couple of times before their persistence paid dividend as Saltou combined with Zubya to half the deficit before the interval.
After a myriad of attack was survived by the visitors, midfield lynchpin Benali got the scores level in the 74th minute but Ighalo would have the final say.
The in-form striker got his fifth goal within four days off his trademark touch to fire Nigeria to the top of Group E.
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