Ighalo scored his first of the night in the 14th minute before turning provider as Ahmed Musa doubled Nigeria’s lead.
The Libyans were not ready to go down easy and pulled one goal back just before the halftime though Mohamed Zubya.
They looked spurred to go on and win it after Ahmed Benali equalised in the 74th minute but Ighalo completed his brace in the 81st minute to get all the three points for the Super Eagles.
Ighalo’s goal ensured that the Super Eagles are now top of Group E of the AFCON 2019 qualifiers.
Super Eagles boss Gernot Rohr made just one change, forced by an injury to Shehu Abdullahi in the first half of their 4-0 win over Libya just three days ago in Uyo.
Ola Aina came on for Abdullahi with Rohr retaining the rest of his starting XI from that game in Uyo for the clash at the Stade Taïeb Mhiri in Sfax in Tunisia.
Playing away from home due to the unrest in their country, the Mediterranean Knights started the game brightly but it was the Super Eagles who got the first chance of the game but Samuel Kalu could not put enough effort on his cross which was well dealt with.
In the 14th minute, however, Ighalo gave the Super Eagles the lead with a tap-in after a one-two between Musa and Alex Iwobi has split the Libyan defence.
Three minutes later, Ighalo turned provider, running at the Libyan defence after picking up a pass on a counter and squaring for Musa who beat three men before finding the net.
The Super Eagles took control of the game with a couple of passes but Libya recovered to ask some questions of the Super Eagles defence.
In the 35th minute. Zubya pulled one back for Libya with a far-post header which beat Nigerian goalkeeper Francis Uzoho.
The Libyans still came at the Super Eagles who were more than happy to hear the halftime hustle.
The Libyans were rampant at the restart, coming at the Super Eagles at every foray forward. In the 74th minute, they got their equaliser through Benali who was on the end of a good move inside the Super Eagles box.
The game was settling for a draw before the 81st minute when Ighalo beat two defenders by feigning a right-foot shot before driving into the box to finish with his left.