Finally, the account got cancelled as predicted and also net banking option got available as suggested by Maribeth and could finally make the payment using one of the savings bank. Please find the screenshot where now it is pending at quickbooks end. Quickbooks team, request you to get this looked on priority and resolved. 

Others, who are facing similar issue-  I would like to bring to notice that please use only savings bank account to make payment and not current account . For current account, it might accept payment(as it did for our case) , but it wouldn't work for it fails internally at their end and which we realised after couple of trials and taking it through quickbooks customer support. 

Further for savings bank account, HDFC Bank savings bank didn't work for me and failed at the end.