As of May 2019, the payment system of the DFA Passport Appointment process is actually not an "online" transaction. So much for an appointment that is created through the internet.
Upon submitting your application, you will receive an email that contains an instruction on how and where to pay. There will also be a reference number that you will use to process the payment:
Related post: I did not receive an email for the appointment code of my DFA online passport application
So, while we wait for the DFA to actually upgrade their system to include credit card payment or at least via mobile banking apps, we'll have to settle to what is available:
To pay in cash via Bayad Center outlets (USSC, 7-11, ECPay, SM, Robinsons, Pera Hub, True Money, Cebuana, etc.) or download Bayad Center Mobile App for both iOS and Android Devices.
I went around Quezon City looking for an actual Bayad Center branch not knowing that I can just tap on that machine inside a 7-Eleven branch! Yes, that's what I did and it worked.
Once paid, you will receive the confirmation email in less than three (3) minutes. I made my payment on a holiday so the email is obviously auto-generated. It also includes an attachment which you will need to print prior to making an appearance to your selected DFA branch to complete your passport application.