Emma Hayes' side trailed 2-1 from the first leg last week but Pernille Harder's 84th-minute header and a very late fourth from Fran Kirby booked a Gothenburg date with Barcelona in two weeks' time.
Kirby had put Chelsea ahead with a goal cancelled out by a stunning strike from Sarah Zadrazil but Ji So-yun restored the lead before half-time.
Arsenal, the champions in 2007, were the only previous English side to reach a final, while Hayes is the first female manager to make it this far since the competition was rebranded in 2009.
Victory also kept Chelsea, who had lost twice in the semi-finals in the last three years, in with a chance of a club double, with the men's team also in the last four.
Chelsea made two changes from the first leg, with the welcome return of captain Magda Eriksson and Niamh Charles also coming in for Jonna Andersson and Guro Reiten.
Bayern were able to recall the prolific Lea Schuller, who was preferred to Simone Laudehr.
The home side began well and were rewarded with a fine goal in the 10th minute, Kirby playing a skilful one-two with Sam Kerr before slotting the ball into the bottom corner.
Only an excellent block from Jess Carter denied Lineth Beerensteyn from equalising five minutes later, but Bayern were level just before the half-hour mark.
It was a moment of real quality from Zadrazil, who picked up the ball 25 yards from goal after a corner had been cleared, took a touch and then smashed it into the top corner.
The visitors had a golden chance to claim a precious second away goal in the 38th minute when Beerensteyn won the ball in midfield and played in Schuller, who shot wide.
Two minutes before the break, Chelsea went back in front through Ji. Her free-kick hit the Bayern wall but, when the ball came back to her, she bobbled a shot past the unsighted Laura Benkarth and into the bottom corner.
Bayern began the second half with greater impetus but more good defending from Carter kept Chelsea in front, and the tension grew as the minutes ticked by.
Chelsea had failed to create another clear-cut opportunity until the 84th minute, when Harder dramatically scored a third goal for the hosts.
A free-kick to the near post from Carter caught out Bayern and Harder nipped in to flick a header into the net.
There was still danger for Chelsea, with one goal for Bayern enough to change the result.
Kerr should have scored another on the break and only desperate defending kept out the Germans, with keeper Benkarth forward, before a break ended with Kirby slotting into an empty net.
Earlier, Barcelona beat Paris St Germain 2-1 for a 3-2 victory on aggregate. All the goals came in the first half. Lieke Martens put Barca two up, Marie-Antoinette Katoto quickly pulled one back but the Catalan side held on.