I sent a message to Booking.com customer service (via the "Get in touch" page) and their reply was approximately as follows.
If you would like to withdraw the entire payment of the facility from
your credit card, please reply to this e-mail and send us your
Once we receive your prepayment request, we will share it with the
premises and, if deemed appropriate, will be withdrawn from your credit card.
I was expecting a self-driven way to pay online, but it seems that there is not without contacting the customer service or the hotel.