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.
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.
Meantime, Mourinho has Sergio Ramos back in his squad for Saturday's match at promoted Real Sociedad (2000) after the Spain defender shook off a muscle problem that kept him out of midweek Champions League action.
Midfielders Kaka (knee) and Fernando Gago (knee) and defenders Raul Albiol (ankle) and Ezequiel Garay (knee) are still unavailable due to injury, the club said on their website (www.realmadrid.com).
Madrid midfielder Xabi Alonso will not be doing any favors for Sociedad, where he played from 1996-2000, although he said he was looking forward to returning to his hometown club.
"There will be three points up for grabs and for the 90 minutes we'll be opponents even though I always have been, and will be, for Real Sociedad," Alonso said. "Going home is always nice and they have always received me very well."
Barcelona coach Pep Guardiola has a full squad available for Sunday's trip to leaders Atletico Madrid (1700) apart from injured striker Jeffren, the champions said on their website (www.fcbarcelona.com).
Barca are looking to get their campaign back on track after slipping up against promoted Hercules last weekend, although Atletico were the only team to beat them last season.
Atletico's Argentina striker Sergio Aguero is racing to be fit after injuring his ankle in last weekend's 2-1 win at Athletic Bilbao.
The Atletico players must not allow Thursday's 1-0 Europa League defeat at Aris Salonika to affect them, according to captain Antonio Lopez.
"They are two completely different competitions and we have to be focused and with our minds on the Barca match," he told reporters.
