If i understand it correctly there was NO charge made to the credit card at the time of the original booking?
In that case there is no right of chargeback via the credit card company.
It depends where the system error was made.
Was a ticket receipt issued at the time of making the booking?
If there was then you can say that payment was deemed to have been made and the flights stated, and the cost of those flights printed on the receipt will be all you need. It is not usual for a recipt to be generated if for some reason the payment was not accepted at the time of booking (for example if the credit card was entered incorrectly or something you should have got an error message at the time).
If no receipt was issued, and no immediate contact was made with Jetstar to ask why the receipt was not issued then there could be some problems.
If a subsequent call was made to Jetstar and they offered to rebook at the full price and that was accepted then again it is a difficult position to argue.
Consumer Affair Victoria has a hotline where you can call and an operator will provide advice there and then on the spot. That would be my first port of call (after Jetstar of course

)
If you agreed to pay the revised price offered by Jetstar i can't see how the credit card company will do a charge back.