Debutants George Ilenikhena and Moses Usor scored for Nigeria, while E. Kari found the net for Madagascar.
Madagascar took an early lead in the 16th minute through Kari, who converted from a pass by R. Ponti.
The Super Eagles responded just before half-time when Ilenikhena struck in the first minute of added time to level the scores at 1-1.
Alex Iwobi provided the assist for the equaliser.
Nigeria completed the comeback in the 65th minute when Usor scored to put the Super Eagles 2-1 ahead.
Semi Ajayi supplied the assist for Usor’s goal.
The result gives Eric Chelle’s side three points from their opening Group L fixture as Nigeria begin their bid to qualify for the 2027 AFCON tournament.
The match was particularly significant for Ilenikhena and Usor, who are among the new players introduced into the senior national team by Chelle for the qualifying campaign.
Both received their first Super Eagles call-ups for the September fixtures against Madagascar and Guinea-Bissau.
Nigeria will next face Guinea-Bissau on September 29 as the Super Eagles continue their Group L campaign.
