Sadio Mane scored twice at the Allianz Arena to put last season's finalists Liverpool through with a 3-1 aggregate last-16 win.
"It's a big step to get this club back on the European stage and I am really happy," said Liverpool's German manager.
"If Barcelona, if Real Madrid come here, they know this is a hard place to win.
"It's a big step for us, let's see what we can do with it, but we have a set a bar for this wonderful club that we really are back on the landscape of top international football.
"We think that is where this club should be, but let's carry on, we have a lot to learn, a lot to improve, but we're back."
Having missed the goalless first leg at Anfield three weeks ago through suspension, Virgil van Dijk's long pass led to Mane's excellent first-half goal.
"His first goal was ridiculous, the calmness with how he's finished it off," Liverpool midfielder James Milner told BT Sport.
"He's on fire at the minute and let's hope it continues for the rest of the season."
Dutch centre-back Van Dijk then headed Liverpool into a 2-1 lead from a Milner corner on 69 minutes after Joel Matip's own goal had handed Bayern a first-half equaliser.
Mane made sure of Liverpool's place in the quarter-final draw by nodding in six minutes from time.
Liverpool's victory means they join Tottenham Hotspur, Manchester City and Manchester United in the quarter-finals, completing a clean sweep of English sides reaching the last eight for the first time since 2008/09.
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"It is good for English football -- that's what you want," added Milner.
"We have good feelings from last year, so hopefully we can carry that on and go as far as we can."
It is a bleaker picture in Germany as Bayern's exit leaves no Bundesliga club in the quarters for the first time since 2005/06, as Borussia Dortmund and Schalke also bowed out in the last 16 -- to Tottenham and Man City respectively.
"Both teams were very cautious for a long period, but the second goal took the belief out of us," said Bayern defender Mats Hummels.
"Jurgen Klopp is good at neutralising the opponents' strengths and he did that once again.
"We didn't play well enough to create enough clear chances at this level."
This is the first time since 2011 that Bayern have failed to make the quarter-finals.
"We have the right to be bitterly disappointed, it's tough not being part of the Champions League anymore," said Bayern head coach Niko Kovac.
"We have to be positive, we have a good run in the Bundesliga and we have to focus on that."
Milner was preferred to Fabinho in Liverpool's midfield, but Klopp was forced into an early change when captain Jordan Henderson hobbled off on 12 minutes.
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Brazilian Fabinho made an early entrance and Milner took the skipper's armband.
"It doesn't look so serious for Jordan's ankle, but it's always a bad sign when you have to make a change, especially in midfield," said Klopp.
Klopp had urged his side to "be brave on the ball" and it was that, combined with an amazing piece of skill by Mane, which gave them the lead.
Van Dijk's pin-point pass over 40 metres found Mane in the Bayern box with goalkeeper Manuel Neuer off his line.
Mane spun away and looped his shot inside the far post to give the visitors a valuable away goal in the 26th minute.
Kovac defended Neuer's decision to come off his line.
"Mane was in the inside track, Rafinha was outside, so it was the right call for Manu to come for the ball," said Kovac.
"However, it shows Mane's quality that he saw where Neuer was and was able to take advantage of it."
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