I'm not convinced, but I think it may mean 'make a payment by means of a debit to your phone account'. This is often done to a mobile (cell) phone's account, but can also be done to a fixed line.
This is a case where language has to be adapted to respond to a new sort of technology. In my book, you can't 'pay' or 'pay in' value, but if that's the way a phone company chooses to express it, I'd better learn pretty fast.
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