Ebay does the charging, as per HMRC regulations. All business sellers, if VAT registered, have to provide their details to ebay, who then notify HMRC. They're trying to combat fraud, but it's all turned into a bit of a mess, with a lot of business sellers walking away.
If you want to claim the VAT portion back, you'll have to approach HMRC directly.
If you'd purchased them from a business directly, they would have zero rated the VAT and marked it for export - which would then be marked on the import forms, so that Australian Customs could charge you themselves.
We shouldn't be advising people to avoid a seller, simply for following the rules.