However, "the revised guidelines also foresee exceptions, which would be applicable for financial stability reasons and on a case-by-case basis", a Commission spokesman said in an emailed note on Saturday.
The spokesman said the Commission had worked closely with the ECB after receiving Draghi's letter and following the entry into force of the new rules "to identify in advance any potential challenges and solutions in implementing the burden sharing rules".
The new EU rules address public outrage at the use of state funds to prop up ailing banks during the financial crisis.
(Read more: Spain to 'come out on top' in stress tests)
Draghi said in the letter mandatory burden-sharing with shareholders and junior bondholders was warranted when a bank was on the brink of collapse or its capital had fallen below the minimum regulatory threshold.
There could be cases, however, when a bank had a viable business model and its capital was above the minimum threshold, but its supervisor still required it to raise additional funds.
In such cases, if the bank could not raise the capital needed in the market quickly enough, the ECB said state aid should be possible without junior bondholder getting hit first.
The letter also said incentives should be in place to ensure that banks did their best to raise private capitals before resorting to state aid.
The ECB is due to take on oversight of euro zone's lenders from national regulators late next year as part of the bloc's plan to adopt a unified system of bank supervision and support, known as banking union.
The ECB will assess lenders' balance-sheets and run stress tests on them before that.
The ECB said on Saturday that the letter Draghi sent to Almunia on July 30 concerned the application of state aid rules to banks that were deemed viable under the balance-sheet assessment but had capital boosting needs when stress-tested.
Italian newspaper la Repubblica reported on Saturday that Draghi wrote to the EU Commission last month asking that junior creditors be spared any losses in a bank rescue at least until the banking union is fully operational.