The Portugal forward angled a shot behind goalkeeper Gianluigi Buffon to score in the fourth minute from a sublime pass by Angel Di Maria.
Juventus midfielder Arturo Vidal then pulled down Sergio Ramos in the area and Ronaldo confidently converted the penalty in the 29th for his seventh Champions League goal this season.
Fernando Llorente had equalized for Juventus seven minutes earlier by squeezing the ball between goalkeeper Iker Casillas and the post in the 22nd. Llorente, a former Atheltic Bilbao player, has now scored six goals against Madrid, including three at the Santiago Bernabeu.
Juventus defender Giorgio Chiellini was sent off in the 48th on a straight red card for hitting Ronaldo in the face with his hand as he vied for the ball shoulder-to-shoulder, but the Portugal forward missed the resulting free kick.
The win gives Madrid nine points from three games and a commanding lead in Group B, where Galatasaray is second on four points and Juventus is stuck on two.
Madrid coach Carlo Ancelotti began the match with Karim Benzema as the sole striker and with Di Maria on the right instead of the benched star signing Gareth Bale. Luka Modric was in the middle and Ronaldo covered the left flank.
Juventus coach Antonio Conte started with Llorente up front, flanked by Carlos Tevez and Claudio Marchisio.
Casillas had to save a stinging shot by Marchisio in the third minute, before Di Maria's masterful pass to Ronaldo sliced through Juventus' flat-footed offside trap to set up the opener - highlighting Ancelotti's difficult choice between playing the Argentina winger or Bale.
Casillas, who has been benched in the league but is Ancelotti's first choice goalkeeper in the European competition, came out quickly to punch out a shot on target by Llorente in the 13th.
Illarramendi then conceded a free kick which Juventus tried score from by playing a rehearsed set piece which Madrid cleared after Tevez missed his shot.
Tevez dribbled past Di Maria on the left flank, rushed into the penalty area and shot just wide of the far top corner in the 15th.
After a period of sustained pressure by Juventus, Andrea Pirlo raced forward and just missed the target in the 33rd with Casillas having to save Tevez's shot a minute later.
Conte reinforced his team's defense by substituting Llorente with Leonardo Bonucci and later by bringing on Kwadwo Asamoah for Pirlo.
Mindful that Madrid is to play archrival Barcelona in the Spanish league on Saturday, Ancelotti substituted Benzema in the 67th to bring on Bale.
Buffon saved a shot from Sami Khedira in the 72nd.