Borussia Dortmund clinched top spot in probably the toughest group in the competition thanks to Wednesday's 4-1 win at Ajax Amsterdam, with nine-times winners Real going through in second after a 1-1 stalemate at Manchester City.
When the last-16 draw is made on Dec. 20, Real cannot be paired with Dortmund or the three other Spanish teams that have qualified - Barcelona, Valencia and Malaga - but will have to overcome one of the group winners.
Possible heavyweight opponents include Bayern Munich, who knocked them out in the semi-finals last season, Manchester United, Juventus, Paris Saint-Germain or Arsenal.
Mourinho, who became the youngest coach to take charge of 100 Champions League matches on Wednesday, noted that his teams had come second in their groups when he won Europe's elite club competition with Porto in 2004 and Inter Milan in 2010.
"Two times I have finished second and gone on to win it," the 49-year-old Portuguese told a news conference.
"I finished second with Porto behind Real Madrid and with Inter I finished behind Barcelona and I won and I have won the group other times and I have not won.
"In my experience it [finishing second] does not mean so much. The teams that finished first will be waiting for an opponent they think may be easier, but if they get Real Madrid that is not good news for them."
100 GAMES
Mourinho was in typically combative mood at City's Etihad Stadium on Wednesday and was obviously furious with referee Gianluca Rocchi for sending off Real fullback Alvaro Arbeloa 20 minutes from time.
The Portuguese clashed with Rocchi during his stint at Inter and was scathing about the Italian's performance.
"I know what Italy is like," he said.
"I was in an Inter-AC Milan derby [refereed by Rocchi] in which we played almost the entire match with 10 and part of it with nine.
"They also gave a non-existent penalty against us and today this happened.
"But I am calm because I have a UEFA sanction hanging over me. And I am grateful to them for the gift they gave me for having reached 100 games in the Champions League."
Mourinho was fined and banned for five matches, two of them suspended for a probationary period of three years, for his behavior during Real's Champions League semi-final first leg against Barcelona at the Bernabeu in the 2010/11 season.
