The Portugal star was today presented with a commemorative shirt by Real president Florentino Perez to mark the accomplishment, and the 32-year-old said: "It's a great honour to reach 100 goals in Europe. Yesterday was a special day, with a very important win.
"I'm very happy. I want to thank Real Madrid for the opportunity to build a wonderful career at this club, and to my team-mates as well.
"Many thanks to the club, my team-mates and the fans."
Cristiano Ronaldo opened up on scoring 100 European goals
Cristiano Ronaldo scored a double last night to make it to 100 European goals
Ronaldo opened his account in Europe while at Manchester United, scoring in a 3-0 over Debrecen in August 2005.
That was Ronaldo's only goal in his first 32 European games for Sporting Lisbon and United, but he has now reached three figures from only 143 matches – all but three of which have come in the Champions League proper.
Ronaldo added: "When I started scoring goals in the Champions League, I never imagined I'd beat this record. For me it's an honour to reach such a difficult figure. I'm absolutely thrilled, really happy."
The striker's brace at the Allianz Arena helped his side recover from going behind to Arturo Vidal's opener, with Vidal also wasting a chance to double the hosts' lead when he missed a penalty.
Cristiano Ronaldo statue is savagely trolled online Wed, March 29, 2017
Cristiano Ronaldo has unveiled a statue of himself outside the airport named in his honour, and Twitter has quickly ripped it to pieces
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Cristiano Ronaldo's statue has been shredded online and even has a Twitter page
Ronaldo levelled in the 47th minute and then, after Bayern saw Javi Martinez sent off just after the hour, the Portuguese superstar netted a 77th-minute winner.
That result has put reigning champions Madrid in pole position to reach the semi-finals, but Ronaldo has warned that there is still work to be done.
He said on his club's website: "We've got a slight advantage and I hope the fans can get behind us and help us, because it's going to be a tough battle. Hopefully Real Madrid win and we get through to the semi-finals.
"We know April will be a difficult, decisive month, and the team looks good. The coach (Zinedine Zidane) has managed things well, with good squad rotation, and we're ready for the final stage of the season."