Substitute Gareth Bale could have sealed it but failed to convert, which left five minutes of added time agony, but Zidane's side held on, with Ramos and Raphael Varane outstanding, to make it to another final in Kiev in three weeks' time.
Kimmich got the scoring started early in Madrid, just like he did in Munich.
To qualify, the Bavarians need to beat Real Madrid by 2-0. Benzema, who has labored through a hard season, was found on the doorstep by Marcelo, and the Frenchman headed home to equalize on the day, capping a 28-pass sequence.
Despite the opening goal coming from Bayern's Joshua Kimmich, it was Real Madrid who secured the victory on the night. Bayern Munich targeted the fullbacks and Casemiro, with James Rodriguez and the wingers often initiating the press. His chance pinged off the bar, though, letting Real Madrid off and keeping the scoreline the same.
"Real Madrid has shown that it can be vulnerable even when playing at home", Bayern coach Jupp Heynckes said through a translator. On top of that, Liverpool have conceded three in only two of their last 36 European away games, while the last time they shipped three goals against anyone was in January's FA Cup defeat to West Brom.
Both teams had chances go begging after that.
Madrid's Navas was regularly in action between the posts but, aside from fine saves to deny David Alaba and Corentin Tolisso, was not tested consistently enough.
The tie should have been put to bed by Ronaldo, but he blazed Marcelo's cross wide with a close-range volley.
The UEFA Champions League semi-final second leg match Bayern Munich vs Real Madrid match will be live telecasted on Sony Ten 2/2 HD.
But it would appear Real Madrid manager, Zinedaine Zidane is planning to get revenge after the Catalan side refused to honour his side after they won the Club World Cup a year ago. Navas was required one more time to stop Bayern from getting a shot off in stoppage time that would have been a sure equalizer, but the Costa Rican came off his line to scoop up the cross.
"We will get some chances and when we get them, we will have to use them", said Bayern president Uli Hoeness.
"But he has scored a lot of goals this season and you can't forget that he once scored four goals against Real in the semi-final of the Champions League for Dortmund". Jurgen Klopp's men take a 5-2 lead into their second leg at Roma on Wednesday.