The Portugal star became the first player in the competition's history to score in 10 consecutive appearances, a run that began when Madrid beat Juve 4-1 in last season's final, before setting up Marcelo to add what could be a crucial third for the reigning champions.
Paulo Dybala was sent off for the hosts in the second half to compound a miserable outing as they suffered their first loss in all competitions since November, and a first at home to Madrid in Europe since 1962.
Ronaldo buried a cross from Isco – who was picked ahead of Gareth Bale by head coach Zinedine Zidane – within three minutes, but Juve were probably the better of the teams in an open first half.
Massimiliano Allegri's side continued to press after the break but Ronaldo struck again in the 64th minute, sending an overhead kick past the motionless Gianluigi Buffon to earn a standing ovation from the home fans.
Dybala received a second yellow card just two minutes later and Marcelo finished a slick move to make it an emphatic win for Madrid, who surely have one foot in the semi-finals despite Ronaldo missing a hat-trick chance in stoppage time.
9 - Cristiano Ronaldo has scored more Champions League goals against Gianluigi Buffon than any other player (nine). Monster. pic.twitter.com/GqJTMaUsQd— OptaJose (@OptaJose) April 3, 2018
Isco wasted little time in justifying Zidane's faith, the Spain star escaping down the left before cutting the ball back for Ronaldo to prod home a clever finish.
100% - Isco (35 passes) is the only player with a 100 percent passing accuracy in the first half of Juventus v Real Madrid. Wizard. pic.twitter.com/TLEDjQMOZY— OptaJohan (@OptaJohan) April 3, 2018
Juve responded well to the setback, with Sergio Ramos making a fine tackle to deny Dybala a clear chance before Rodrigo Bentancur scuffed a shot after being teed up by Gonzalo Higuain.
Higuain thought he had levelled against his old club 22 minutes in, but a brilliant reaction save from Keylor Navas denied the striker from close range, before Toni Kroos blasted a shot off the crossbar on a rare Madrid break.
Juve felt they could have had two penalties just before half-time, but referee Cuneyt Cakir decided Casemiro did not deliberately handle a Giorgio Chiellini header and then booked Dybala for diving when he went to ground easily in the box.
The home side continued to press early in the second half, Dybala watching a free-kick deflect agonisingly wide after a foul by Ramos, who picked up a booking that will keep him out of the second leg in Spain.
The match was taken out of Juve's hands in the space of two minutes. Ronaldo acrobatically fired Dani Carvajal's cross into the net from 12 yards out, earning applause from all corners of the Allianz Stadium, and Dybala's high foot on Carvajal saw him dismissed soon afterwards.
With the home crowd stunned, Marcelo combined first with Isco and then Ronaldo before clipping the ball over Buffon and blasting home on the line with 18 minutes remaining.
Mateo Kovacic hit the bar from the edge of the box and Ronaldo missed a golden chance to get his third, volleying over unmarked from barely six yards out, but the damage had been well and truly done.
Key Opta stats:
- Cristiano Ronaldo scored his 39th goal in all competitions this season – more than any other player in Europe's big five leagues.
- Juventus conceded three goals in the home leg of a Champions League knockout tie for the first time since their 1999 semi-final defeat against Manchester United (3-2).
- Ronaldo has scored 22 goals in the quarter-final stages of the Champions League – more than opponents Juventus have (21).
- Paulo Dybala's red card was Juventus' 24th in Champions League history – at least five more than any other team.