Joshua Kimmich struck had in the third minute of the game to restore parity.
They have, however, taken heart from the way Juventus overturned a 3-0 first leg deficit in their quarter-final return fixture in Madrid, before Cristiano Ronaldo netted a stoppage time penalty to send Madrid through.
"We have had a wonderful atmosphere, a great collaboration over the nine months, it's a group that has character, it's a pity it was not rewarded", he added.
"It's the first time we weren't realy as good as we can be".
Benzema's two goals here were another feather in the cap for coach Zinedine Zidane, who had made a decision to start the French striker, despite only one goal in his previous 12 games.
Bayern, meanwhile, were without a host of star players, with Javi Martinez, Arturo Vidal, Arjen Robben, Jerome Boateng, Kingsley Coman and Manuel Neuer all injured.
"I'm delighted for him, it was exactly what he had wanted to do for so long, to score, he did it twice and gave us the possibility to go through", said Zidane.
His Bayern team went down fighting in Madrid.
Zinedine Zidane's side continue to rewrite the history books, with the club preparing for a third successive final and a 16th in total - with their manager yet to suffer a defeat in continental knockout competition.
"Messi and Ronaldo are different players, both in the highest level and each one deserves good words from everyone".
Marcelo admitted he was fortunate not to concede a penalty.
Joshua Kimmich scored for Bayern in the third minute to set the stage for another comeback at the Santiago Bernabeu, like the one Juventus almost pulled off in the quarterfinals before Ronaldo converted an injury-time penalty. "Anything can happen in football, Roma still have a chance", he said after the game. "During the course of your career, you have your ups and downs, but they've shown that they can be relied upon at key times".
"It's a bad thing for a player to live through", said Bayern coach Jupp Heynckes. Real, out of sight in La Liga, were outplayed by Bayern for much of the tie, with the Germans reeling off 39 shots across the two games to their 16. Maybe that is a quality, not to make mistakes that big. "If I tell you that the ball has not touched my hand, I'm a liar", Marcelo said afterwards. "But Navas was outstanding".
Jupp Heynckes retired to Bayern Munich in the semifinals of the Champions League with the coach admitting that not numerous 72 years can experience "such an adventure".
"We played better than in Munich".
Either Liverpool or Roma will prove hard opponents for Los Blancos in Kiev, with a third consecutive trophy anything but a formality.