Real's superstar then hit the victor as substitute Marco Asensio, on for Bale, put in a low pass for Ronaldo to tap the ball home between Neuer's legs.
Bale is being sat out with a calf niggle and his fellow front-men will also be rested for the La Liga clash.
Bayern's Philipp Lahm looks at Real Madrid's Cristiano Ronaldo celebrating with teammates scoring his side's 2nd goal during the Champions League quarterfinal.
Fabio Coentrao could make only his second league appearance of the season after recovering from injury.
Real may also leave with regrets, as they could have taken a commanding lead into next week's second leg at the Bernabeu.
Real capitalized on their numerical advantage and sealed the deal in the 77th minute when Ronaldo wrapped up his brace after slotting home Marco Asensio' s cross to become the first player who reached 100 goals in an UEFA club competition.
Vidal came close to adding a second not long before the interval, too, when Arjen Robben squirmed his way down the right flank and to the goal line before his cross was headed just wide of the net by his Chilean team-mate. "We probably could have scored one or two more goals, but we're very happy", the Real coach said at a press conference.
Ronaldo had scored twice in his previous eight Champions League games and had failed to find the net in any competition for a month but on Wednesday he netted twice either side of halftime to end the German champions' run of 16 straight home wins in the competition. "We would have preferred to have scored another goal", Real Madrid coach Zinedine Zidane told French TV.
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If not, we will solve the problem without them! Kim Jong Un didn't speak before North Korean television ended the live broadcast. According to a report by The Washington Post , Chinese Foreign Minister Wang Yi said that "storm clouds" were gathering.
"We know that it's a very important game and we're going to have to produce a great performance if we're to put any points on the board".
Before scoring his first goal of the night, Ronaldo had gone 659 minutes without scoring in Europe, but he insisted he was unaware of any doubters. "We'll have to see what his injury is", Zidane said. I'm over the moon and so happy. But a penalty miss just before half-time from opening goalscorer Arturo Vidal, Ronaldo's equaliser and then a red card for Javi Martínez turned the game.
"We hope he is back with us in a short time".
"I thought it was going to be a complicated match but after they missed the penalty I was convinced that the team would be encouraged", he continued.
"I trained hard to be playing well in this final month and a half of the season", Ronaldo said.
"We had the chance of having a good 45 minutes".
More than half of his strikes have come in the opening 45 minutes of games, with his one and only extra-time goal helping Real clinch the trophy against city rivals Atletico Madrid in 2014.
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