Leading 3-0 from the first leg at Stamford Bridge in February before the coronavirus pandemic halted the competition, treble-chasing Bayern underlined their dominance to progress 7-1 on aggregate.
The Bundesliga and German Cup champions will meet Barcelona next Friday in Lisbon for a place in the semi-finals.
Lewandowski netted a penalty with just 10 minutes gone at the Allianz Arena. Winger Ivan Perisic then doubled Bayern's lead before England striker Tammy Abraham tapped home a loose ball to give Chelsea brief hope.
However, replacement midfielder Corentin Tolisso put the result beyond doubt when he fired home a Lewandowski pass with 14 minutes to go.
This was a world-class display from Lewandowski who played a hand in all four goals, adding a late header to his pair of assists.
After a ruthless display in the first leg, Bayern picked up where they left off six months ago.
They took the lead when Serge Gnabry, who scored twice in London, spotted the run into the box of Lewandowski, who was tripped by Chelsea goalkeeper Willy Caballero.
The Poland striker was initially flagged offside, but VAR ruled otherwise. Caballero was booked and Lewandowski converted the resulting penalty for his 12th goal in seven Champions League games.
He turned provider on 24 minutes as Bayern kept up the pressure.
After Mateo Kovacic lost possession near the halfway line, the ball was worked to Lewandowski who squared for Perisic to fire home.
Former Bayern target Callum Hudson-Odoi, who was linked with a move to Munich at the start of the season, beat Manuel Neuer on 28 minutes only for the goal to be ruled out by VAR for an offside.
However, Chelsea pulled a goal back just before half-time.
Bayern goalkeeper Neuer could only parry a shot by Hudson-Odoi and Abraham tapped home the loose ball on 44 minutes to make it 2-1 at the break.
Mason Mount forced Neuer into a low save early in the second half, while Bayern lost defender Jerome Boateng to a leg injury with an hour gone. He was replaced by Niklas Suele as Perisic made way for Brazil playmaker Philippe Coutinho.
Bayern coach Hansi Flick also changed both defensive midfielders, Thiago Alcantara and Joshua Kimmich, for the final 20 minutes.
It paid off two-fold as moments later Tolisso, on for Alcantara, made it 3-1 when he turned home Lewandowski's pass on 76 minutes.
Alvaro Odriozola, on for Kimmich, then supplied the silky cross on 84 minutes which Lewandowski headed home for his 53rd goal in 44 games this season.