Guinea-Bissau had taken firm control of the group after handing the Super Eagles a 3-0 defeat in their Matchday Two fixture last month.
However, the Djurtus were unable to secure all three points against Madagascar, needing a late equaliser to avoid defeat.
Warren Caddy put Madagascar ahead a minute before the hour mark, but Galatasaray forward Renato Nhaga restored parity for Guinea-Bissau six minutes from time.
The draw presents Nigeria with an opportunity to close the gap at the top of the group when they take on Tanzania’s Taifa Stars in Uyo on Friday.
A victory for the Super Eagles would strengthen their position in the race for qualification and keep their hopes of securing a place at the 2027 AFCON firmly alive.
