The directive is designed to reduce the risk of double or non-taxation due to different national rules, the Council said.
These 'mismatches' occur when vouchers are issued in one state and used in another, and when they are traded, the Council said.
"Vouchers are used increasingly and come in many forms. They include, for instance, pre-paid telecom cards, gift cards and price discount coupons for the purchase of goods or services," it said.
The directive gives a definition of what a voucher is, and gives rules on how to determine the taxable value of single- and multi-purpose vouchers, the Council said.
Single-purpose vouchers will be taxed when they are sold, as they can only be used to buy one type of good or service that is subject to a set rate of VAT. Multi-purpose vouchers may be used for different goods, so must be taxed when they are used.
The rules only cover vouchers that can be used for redemption against goods and services, and not those offering a discount. The provisions should not trigger any change in the VAT treatment of transport tickets, admission tickets to cinemas and museums, postage stamps or anything similar, the directive said.
This directive is "narrower in scope" than a previous European Commission proposal in 2012, the Council said.
Member states have until the end of 2018 to include the directive in national laws, and its provisions will only apply to vouchers issued after that date, the Council said.
The UK introduced VAT on phone cards and certain other vouchers in 2012.