The 32-year-old led Madrid to LaLiga glory and the successful defence of their Champions League crown in 2016-17, but has struggled for goals in domestic competition this season with just two league strikes to his name.
Dortmund equalized with two goals by Pierre-Emerick Aubameyang, one in each half, but Lucas Vazquez got the winner in the 81st minute at the Santiago Bernabeu Stadium.
Raphael Varane limped off in the first half and appears highly unlikely to return in time for Saturday's La Liga clash with Sevilla. "We won the league and the Champions League, where I was again the top scorer", Ronaldo told French daily L'Equipe. "I scored, I helped the side win".
Making things more difficult is that Borussia Dortmund are badly shorthanded thanks to injuries - Maximilian Philipp, Gonzalo Castro, Mario Götze, Łukasz Piszczek, Erik Durm, and Sebastian Rode are all out, while Jeremy Toljan is suspended.
Arsenal and Manchester United were the last two English teams to reach a 16-point tally in the competition at the group stage and went on to reach the final in 2006 and 2007 respectively.
"He is great player and with his speed he is always a dangerous player", said Dortmund boss Peter Bosz. "He's aggressive. It's brilliant for any football fan to watch". They pass from one side to another, run, defend.
In the 12th minute, Ronaldo curled a stunning ball around goalkeeper Roman Burki.
Vazquez' winner came with a low shot from just outside the area after being set up by Theo Hernandez with a header.
"Portugal always had talented players in the past, but they didn't believe they had a chance when they faced the big national sides like Brazil or Germany", said Portuguese sports commentator Luis Freitas Lobo. "I think that's good for our confidence".
Dortmund will turn its attention to the Europa League after finishing third in the group, 11 points behind second-placed Madrid and 14 adrift of table-topper Tottenham.
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