The Falconets booked their place at the showpiece, advancing 8-0 on aggregate, thanks to braces from Nduru Ndidi, Rashidat Ajibade and Anam Imo at Samuel Ogbemudia Stadium in Benin City.
Nigeria will be making their sixth straight appearance at the event, taking place in France from August 5-24.
Basetsana have never qualified for the tournament.
“You still have age on your side and have done well to reach this stage of the qualifiers. The result did not go our way but that does not mean that you are failures. You fought hard like true champions and should you keep that spirit, you have a good future in football,” said Khumalo.
She also thanked SAFA for entrusting her to steer the side.
“I would like to thank our football association for trusting me with such a big task of coaching a national team. It is something I do not take lightly. The experience and lessons learnt will certainly go a long way in contributing to the growth of women’s football in our country.”