You can charge VAT on Ebay sales, but it has to be included in the sales price on the listing.
You don't seem to have your VAT number registered with Ebay though. It usually shows in the contact details if you have. Without having that registered I don't know if you can do an invoice with VAT shown seperately. Also once an item is paid for you usually can't send an ebay invoice.
There's infomation on registering your VAT number with Ebay on the help page below. Then you will also be charged your ebay fees net of VAT.
http://pages.ebay.co.uk/help/account/vat-business.html
You could try asking your question on the business seller's board to see if anyone there has any further suggestions about the VAT invoice.
http://community.ebay.co.uk/forum/Business-Seller-Board/1900001545?