If the customer has provided permission for you to charge their credit card on file, you can manually get the invoice paid off using their stored payment accounts.
On your reseller portal, locate the "Invoice" (ref 1.) in the “Customer Invoices” (ref 1.) tab and select it.
Click on the “Pay this invoice” (ref 4.) button on the top.
When asked to make the payment, select “Pay with stored payment accounts” (ref 1.).