The £80million man reached the landmark haul on just his 105th appearance for the Spanish giants after leaving Manchester United two years ago.
Ronaldo's brace sealed Madrid's place in the last 16 of the tournament and left boss Jose Mourinho purring over his star player.
The Special One said: "It is an incredible record. To score 100 goals for Real is tremendous, especially scoring two goals here in Lyon where we have a negative record historically. I think it's fantastic."
Portugal superstar Ronaldo opened the scoring in the 24th minute by curling home a free-kick.
And he became a Real centurion on 69 minutes when he converted a penalty after Lyon fullback Mouhamadou Dabo had fouled him.
The win put Madrid top of Group D on 12 points — five clear of second placed Ajax, who thumped Dynamo Zagreb 4-0.
But the night belonged to Ronaldo, who is battling Barcelona's Lionel Messi for the World Player of the Year crown.
Argentine ace Messi hit a hat-trick last night in the 4-0 victory at Viktoria Plzen — taking his tally to an amazing 202 goals in 286 matches for the reigning Spanish and European champions.
Fuck, 80m really well spent
Amazing
no big deal lah......................
Alexander Duric can do it too