Mourinho was approached by Portugal's football federation (FPF) and asked if he would take over for the qualifiers at home to Denmark on Oct. 8 and away to Iceland four days later.
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He told a news conference at Real's training ground on Friday he was unable to accept the offer as he believed his club would not have reacted positively to his absence.
"For personal pride and passion for Portugal I couldn't say no but I can't say yes either," Mourinho said.
"My sense is that in the Real Madrid world it would have been interpreted negatively," he added.
"There would have to be total agreement and I don't think that's going to happen. Real Madrid has every right to make the decision they have. For me the issue is finished."
Portugal sacked Carlos Queiroz this month after he was suspended for six months for insulting anti-doping agents before the World Cup and have yet to name a replacement.
They have had a poor start to their qualifying campaign, with a 4-4 home draw against Cyprus and a 1-0 defeat in Norway.
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