The Rangers striker had said he would accept a call to represent Scotland.
And England coach Fabio Capello was thought to be keen on picking Spaniards Manuel Almunia and Mikel Arteta.
But the Scottish Football Association has confirmed that the Home Nations would continue to pick players based only on bloodlines.
Novo, 29, has spent eight years playing in Scotland and admitted he would consider applying for a UK passport and switching allegiance to his adopted country, if asked.
Scotland manager George Burley refused to rule out the option of picking Novo, while SFA president George Peat was opposed to any change to the current criteria for selection.
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"There has been some confusion and much debate in recent days about whether or not Nacho Novo can play for Scotland," said SFA chief executive Gordon Smith.
"On one hand, the Fifa regulations say that George Burley can pick eligible players who hold a British passport - and, on the other, we have the gentlemen's agreement with the other Home Associations that says that we will pick players based on their bloodline.
"I have sought to clarify the issue. We have had discussions with the other associations in the past couple of days and I've found out that everyone is adhering to our agreement and that, subsequently, we're all going down the line that we will use bloodline as the basis for eligibility.
"Now, at some stage in the future, one or more of us may change our opinion on that - we may get together and change our decision and go for the full Fifa regulation - but, at the moment, we're all sticking to our agreement."
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