Hello Sir,
Here is my reply to your query:
You can make the payment of penalty under section 272A(1)(d) while filing your income tax return though the online means.
In case you are filing the return Online then income tax website will automatically take you to the website on which this amount can be paid though debit card or net banking.
In case you are filing the return offline then you have to visit this below given link to make the payment.
https://onlineservices.tin.egov-nsdl.com/etaxnew/tdsnontds.jsp
Thanks and Regards
Divya Chugh