The Portuguese attacker grabbed a brace to ensure the Spanish giants reach the knockout stages of Europe's elite competition, despite two fixtures still left to play in Group D
Ronaldo grabbed his first goal of the game in the 24th minute with a thunderous set-piece from just outside the penalty area in a game that Madrid dominated. He added his second of the evening and his century goal for Madrid in the 69th minute from the penalty spot.
The result leaves the Spanish club on 12 points at the top of Group D and maintains there 100 per cent record in the competition with the Spaniards yet to concede a goal in their opening four fixtures.
Lyon remain in third place, three points behind Ajax with the two teams due to meet in a fortnight and the French team in need of victory against Frank de Boer's men.
After a nervy start, Madrid could have taken the lead in the 10th minute yet Lloris made a superb save to deny Jose Mourinho's men. Mesut Ozil played a precise throughball to Karim Benzema who saw his shot from 12 yards tipped brilliantly over the bar by his international team-mate Hugo Lloris.
The away side took a deserved lead in the 24th minute after they were awarded a free-kick on the edge of the box following a foul on Benzema. Ronaldo stepped up to smash the ball through the wall and into the far corner, past the flailing attempts of Lloris in the Lyon goal - the Portuguese attacker's 99th goal in the white shirt of Madrid.
However, despite the away side looking the better team, Lyon nearly drew level in the 46th minute. Bafetimbi Gomis slid the ball through to Yoann Gourcuff who saw his effort just inside the box expertly turned over the bar by Iker Casillas to preserve his team's lead at half-time.
After weathering a short renaissance from Lyon at the beginning of the second half, Ronaldo scored his second of the evening and his 100th for Madrid after Mouhamadou Dabo fouled the former Manchester United man in the box on 69 minutes. Ronaldo coolly stepped up to dispatch the ball into the far corner, despite Lloris diving the right way.
The away team were given a late scare in the 78th minute when Gourcuff's corner was met by the head of substitute Alexandre Lacazette who could only watch on as his effort bounced back off the crossbar, with Madrid holding on for all three points in France.
Next up in Europe for Mourinho's side is the visit of Dinamo Zagreb to the Bernabeu on November 22 while Lyon travel to Ajax on the same evening - desperate for a positive result to keep their qualification hopes alive.