Pay Whole Cart amount including shipping and taxes via third party app

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We are developing an application where in the customers on our site will earn for their orders. The customers can also redeem their earnings on our site. 

However we are facing issues during the redemption process.

My question is how can I let  the customers of our site pay via their earnings on a third party app?

Below are the approaches we already tried  and their limitations that we are facing:

1. Generate a discount code for the amount and  use that for payment ( However this method doesn't requires the customers to pay their taxes and  shipping charges. Whereas our requirement is to be able to make a full payment via our third party earning points)

2. Generate Gift card (We are not using shoify plus)

3. Using APIS  (Graph or REST) to mark checkout as complete - This doesn't complete checkout  from backend. it requires users to click on some url and process checkout We are looking for a complete backend solution wherein we can complete the checkout and create order and mark it as paid.


Any help?