When did you come to know about approval for the extension of your tenure? You could have applied immediately for the extension of maternity leave.
Anyway, even now also you may apply for the extension of the maternity. Since the delivery is already over, you may submit the certificate from the hospital authorities about your delivery. In case if you have obtained the birth certificate for a newly born child from the local municipal office, then you may attach that also.
Address your application to the head of the institute however, route your application through the proper channel.
By the way, heading of your post is misleading. Your maternity leave was sanctioned until the end of your tenure. Therefore, the authorities cannot be blamed per se for not adhering to the provisions of the Maternity Benefits Act, 1961. If you were not eligible to get maternity leave after 30th May 2019, then how the approving authorities would have sanctioned it? Institute authorities have done what best they could have done.
2nd June 2019 From India, Bangalore