Goals from debutants George Ilenikhena and Moses Usor secured a comeback victory for the Super Eagles at the Godswill Akpabio International Stadium, Uyo.
Eric Chelle's men started the keenly contested match brightly as they created clear opportunities while the Barea defended resolutely and looked dangerous on the counter.
However, it was the visitors who stunned the home crowd in the 16th minute when Clement Couturier headed home Ryan Ponti's cross past goalkeeper Stanley Nwabali.
That fuelled a positive response from Nigeria who attacked in number with Saudi based Ilenikhena going close on two occasions.
His first effort was saved by goalkeeper Geordan Dupire after being played through by Calvin Bassey before heading over the bar from Samuel Chukwueze’s cross.
The Super Eagles eventually found an equaliser in first-half stoppage time with Ilenikhena tapping home from close range after a brilliant pass from Alex Iwobi to send the teams into the break level.
Nigeria returned for the second half with greater attacking intent and continued to search for a second goal. Ademola Lookman had an effort blocked inside the box, while Bassey also saw a header saved by Dupire.
Chelle then turned to his bench, bringing on Moses Usor for Chukwueze and centurion Moses Simon for Akor Adams.
The substitutions quickly paid off as Usor put the three-time African kings ahead for the first time in the 65th minute.
The LASK forward received the ball from Semi Ajayi, drove forward, beat two defenders and cut inside before firing a left-footed effort into the bottom-right corner.
Madagascar pushed for an equaliser, but Nigeria held firm during the closing stages. Hakim Abdallah had an effort blocked as the visitors continued to threaten.
Chelle made further changes, with Tolu Arokodare replacing Lookman and Taiwo Awoniyi coming on for Ilenikhena as Nigeria protected their lead.
The victory gives Nigeria three points from their opening qualifier, while Madagascar returned home with heads bowed low.
The Super Eagles will next travel to face Guinea-Bissau, who opened their campaign with a 2-0 away victory over AFCON 2027 co-hosts Tanzania to move to the top of Group L.