Eric Chelle’s men fell behind early after Madagascar punished a quick transition to beat goalkeeper Stanley Nwabali.
However, debutant George Ilenikhena restored parity in stoppage time before the break while substitute Moses Usor then completed the comeback with a fine solo finish to secure all three points.
Adepoju said collecting maximum points remained the key objective despite the early setback.
“It’s a good way to start the qualifier with a victory, not minding that we conceded first. The most important thing is that the team won against Madagascar,” he told Completesports.
“I am delighted that we have so many options that can play for the Super Eagles and that’s a very good development.
“It is left for the coach to know who he wants to start… He knows the composition of the team right from the beginning and will definitely know who to start.”