Bayern, who have won the competition four times in all and reached the final on three further occasions, will play either Inter Milan or Barcelona at the Bernabeu, the home of Real Madrid.
Lyon have never reached a European showpiece and they scarcely looked like wresting back the advantage as they produced an even more insipid display than they had in the first leg in Munich last week.
They failed to respond to the sizzling pre-match atmosphere inside the Stade Gerland as Bayern - who barely got out of first gear themselves, or needed to - set the tempo from the first whistle.
Knowing an away goal would give Lyon a mountain to climb the Germans - missing suspended winger Franck Ribery - almost got off to a dream start, but after Olic stole the ball off Cris his pass to Mueller was slightly behind the 20-year-old and he could only shoot wide.
Lyon, with haphazard defending and misplaced passes coursing through their play, simply could not get going as they looked more like the side sixth in the French league than the team that knocked out Real Madrid in the last 16.
With 26 minutes gone, Bayern got the goal that effectively settled the tie as Mueller played a lovely one-two with former Chelsea winger Arjen Robben down the left and crossed for Olic to turn inside a defender and fire past Hugo Lloris.
Olic hammers his second past Lloris
Now requiring three goals to progress, Lyon needed an immediate response and they should have had it when Sidney Govou crossed for an unmarked Michel Bastos six yards out, only for the Brazilian to woefully volley wide.
The French side's coach Claude Puel sent on £11m striker Bafetimbi Gomis at the break but after he ballooned a volley over from six yards, any hopes the hosts had quickly evaporated.
Cris was perhaps harshly booked by Swiss referee Massimo Busacca for a foul on Olic and when he sarcastically applauded the decision, a second yellow card and a red followed soon after.
Lyon initially responded well to what the home fans felt was an injustice as Govou stung the palms of Hans Jorg-Butt, but the game was well and truly over when Altintop played a stunning reverse pass for Olic to fire past Lloris.
It only remained to see how many Bayern could score and after Lloris tipped away Robben's drive, Olic completed a fine hat-trick by superbly heading home Lahm's right-wing cross.
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