The Super Eagles struggled to threaten their counterparts from the island nation in the opening stages of the match.
Nigeria fell behind in the 16th minute when Ehsan Kari headed Madagascar into the lead, with the effort beating goalkeeper Stanley Nwabali.
The Super Eagles struggled to threaten their opponents in the opening stages, although Nigeria tested Madagascar goalkeeper Geordan Dupire with a shot from the right flank in the 28th minute.
Wilfred Ndidi then headed over the bar a minute later.
Nigeria appeared to have equalised in the 33rd minute when Alex Iwobi found the net from inside the 18-yard box, but the goal was ruled out after the referee pointed to a foul by Akor Adams on Dupire.
The Super Eagles eventually drew level in the 45th minute through debutant George Ilenikhena.
The Al Ittihad forward finished off an Alex Iwobi pass before driving the ball into the net.
The equaliser sent both teams into the break level, but Nigeria returned for the second half with greater attacking intent.
The Super Eagles recorded 21 touches in Madagascar’s box early in the second half, compared with three by their opponents.
Madagascar came close to restoring their lead in the 51st minute, but Nwabali comfortably dispossessed Rayan Raveloson.
Nigeria coach Eric Chelle made his first changes in the 61st minute, bringing on Moses Usor and Moses Simon for Samuel Chukwueze and Akor Adams.
Usor made an immediate impact, scoring Nigeria’s second goal just minutes after coming on to put the Super Eagles ahead.
Chelle subsequently strengthened the attack with the introduction of Taiwo Awoniyi and Tolu Arokodare in the 69th minute.
The Super Eagles held on to secure the three points and open their 2027 AFCON qualifying campaign with a victory.
The tournament will be hosted by Kenya, Tanzania and Uganda in 2027.
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