The Football Association of Wales had asked UEFA to change their rules and allow the exile clubs into the Europa League via the Welsh Cup if they opted out of the FA Cup but the request was turned down at a meeting of the governing body's executive committee in Istanbul.
FAW chief executive Jonathan Ford told Press Association Sport he was "bitterly disappointed" by the decision.
Wales also lost out to the Czech Republic in their bid to host the 2015 European Under-21 Championships.
UEFA also announced that a possible legal loophole in their financial fair play (FFP) rules has been closed after signing a joint agreement with the European Commission that the regulations are fully compliant with European law.
The FFP rules state clubs in European can only spend what they earn but it had been suggested that overspending clubs could challenge that in the European courts.
UEFA's general secretary Gianni Infantino said: "Let us be clear this is not a new law. But it re-affirms what we have always said that the FFP rules are legal and in accordance with European legislation."
UEFA also agreed to consider a new bid by Gibraltar to become a member and take part in European competition - something that has been fiercely opposed by Spain.
The British colony, which has a population of 28,000, wants to become UEFA's 54th member and their bid will be decided at next year's UEFA Congress in London.
Spain claim sovereignty over Gibraltar and when they last bid in 2007 the Spanish threatened to withdraw from any competition to which Gibraltar were admitted.