It sounds as though you arranged this return privately with the seller, without using eBay's money back guarantee. If you had used the procedure that eBay provides you would have received a full refund.
As you chose to negotiate with the seller yourself there was no point in trying to "get eBay involved" because if you if you don't follow their procedures they are not involved.
It might be that you could belatedly still open a case, but you would have to take this up with eBay customer support. Otherise, as you say, it may be simpler to contact your payment provider. In the circumstances even this may not be entirely straightforward, but good luck anyway.
In future, I would strongly recommend you to read and use eBay's money back guarantee. In most cases it provides very good protection and is easy to use.