As nouns the difference between invoice and waybill is that invoice is a bill; a commercial document issued by a seller to a buyer indicating the products, quantities and agreed prices for products or services that the seller has already provided the buyer with an invoice indicates that, unless paid in advance, payment is due by the buyer to the seller, according to the agreed terms while waybill is a document that lists the final destination (and other details) of each part of a cargo.

As a verb invoice is to bill; to issue an invoice.