Goods imported from outside the EU and sold online for less than 22 euros (26 dollars) will no longer be exempt from VAT under the new system.
The European Commission says the set of changes will cut red tape for sellers and help tackle VAT fraud - estimated to cost 7 billion euros a year.
The update - the first since 1993 - also includes the creation of a "One Stop Shop" platform for both EU and non-EU sellers.
At present, EU traders selling to other member states have to register in each country where they sell. Now they will only have to register once, on the "One Stop Shop," in order to pay VAT for sales within the bloc, according to the commission.