A depleted Blues side missed the services of Cesar Azpilicueta, Willian, Christian Pulisic and Pedro. Meanwhile, want-away midfielder Thiago Alcantara featured for Bayern.
Drama early on resulted in a spot kick to Bayern after Willy Caballero hacked down Robert Lewandowski, with the Video Assistant Referee concurring with the man in the middle. The Polish striker had no problems beating Caballero from the spot and further prolonging their healthy advantage in the overall tie 10 minutes in.
Ivan Perisic put the German giants in total ascendancy two minutes following the midway phase after cropping up on the right-inside channel to fire beyond Caballero.
Chelsea looked to have levelled before the half-hour mark after Callum Hudson-Odoi drilled a 20-yard scorcher past Manuel Neuer, only for the flag to go up following an offside in the build-up.
Tammy Abraham put the Blues on the score-board a minute to halftime after capitalising on Neuer's error for a rather simple execution.
Chelsea were out in full force in the second half, with Mason Mount bringing Neuer to a smart save from a tight angle after landing onto Emerson Palmieri's ball.
Thomas Muller missed a clear chance to get his name on the score-board after misfiring Alphonso Davies' ball from out wide 61 minutes gone.
Bayern introduced a couple fresh faces shortly towards the final sector of the match as Phillipe Coutinho and Niklas Sule came in for Perisic and Jerome Boateng respectively.
Bayern put the match beyond doubt with 14 minutes remaining when Corentin Tolisso volleyed straight through Caballero from an unmarked position following Lewandowski's supply.
There was time for a fourth goal as Lewandowski nodded home his second seven minutes from time following Alvaro Odriozola's delivery, as Bayern cruise into the quarter-finals.