The Portuguese, who spent six years at United from 2003, completed a 2-1 win for Real who went through to the Champions League quarter-finals 3-2 on aggregate.
He received a rousing welcome back before the match, but broke the home fans' hearts when he slid in at the far post after 69 minutes to sweep the ball into the net.
"It was an emotional moment for me. I just have one word to say - unbelievable. What the supporters do to me is they make me feel shy," Ronaldo, who also scored Real's equaliser in the first leg in Madrid, told Sky Sports.
As a mark of respect to the United fans who once adored him, he pointedly refused to celebrate his winner, shrugging his shoulders and lifting his arms as if to say sorry.
"It's respect for the affection that people gave me here over many years. Those are feelings that you don't forget," he added on Spanish television broadcaster TVE.
"I didn't celebrate but I was happy inside and what I wanted most was to win and step by step continue on our way to the final of the Champions League."
Before the match United manager Sir Alex Ferguson remembered what the great Brazilian striker Ronaldo did for Real against his team a decade ago, when he scored a hat-trick at Old Trafford to help the Spaniards into the semi-finals.
"Our main worry," said Ferguson on Monday, "was not what happened 10 years ago but what is going to happen tomorrow."
He was right to be worried.
Tuesday's win completed a remarkable week for Real who beat arch rivals Barcelona in La Liga and the King's Cup before toppling United.
The match turned when United, 1-0 up and in control, were reduced to 10 men as Nani was harshly sent off for raising his foot to Real defender Alvaro Arbeloa after 56 minutes.
Ronaldo said he did not see the incident and all that really mattered to him now was success with Real.
"I helped my team to score one at home, one away," he added. I didn't see the replay of what Nani did, but it's situations that happen in football."
He also distanced himself from media speculation that he might be returning to his former club.
"The United supporters here and the club - it's massive but at the moment I'm very happy at Real Madrid and want to be there," he said.
"It was an unbelievable week. We won both games against Barcelona and Manchester United. We're in good shape and want to carry on like that."
Five years ago Ronaldo won the Champions League with United, scoring in the 1-1 draw in the final against Chelsea in Moscow but missing a penalty in the shootout.
After seeing off United, a second winner's medal has come a big step closer.
Get the best features, fun and footballing frolics straight to your inbox every week.
Thank you for signing up to Four Four Two. You will receive a verification email shortly.
There was a problem. Please refresh the page and try again.