An ex friend who is currently waiting for a response/approval of his expired work permit refuses to pay me money that he borrowed. I have evidences that he used my visa to pay for his application fees but now he's denying any of it. I want to at least get my money back or if not get him deported.

You can not get him deported. He is already working with immigration on visa status.

You allowed him use of your credit card ? Or did he steal it ?

If he stole your card, report it to police.

But you sue him in civil court for the money, just like you sue anyone else.