The West Africans entered the Group L encounter with maximum points from their opening two matches but struggled to overcome their determined opponents.
Following a goalless first half, Warren Caddy handed Madagascar the lead in the 59th minute.
However, Guinea-Bissau responded strongly and eventually restored parity six minutes from time through Renato Nhaga, who converted following an assist from Tombie Vieira.
The late equaliser ensured the visitors maintained their unbeaten record while denying Madagascar a crucial victory in their qualification campaign.
Guinea-Bissau now have seven points from three matches and remain well placed in Group L.
Both nations will renew their rivalry on November 17, with Madagascar hoping to revive their qualification ambitions.