Dortmund, beaten 2-1 by Stuttgart at the same venue in November, were outclassed by a dominant home side who won thanks to second-half goals from Serhou Guirassy and Silas.
Guirassy now has 18 goals in 13 games in all competitions this season.
English teenager Jamie Bynoe-Gittens had the ball in the net for Dortmund shortly after Guirassy’s goal, but the effort was ruled out by VAR for offside.
With Dortmund pushing for an equaliser, Stuttgart striker Silas carved through some sleepy defending to score a second and seal his side’s progress to the quarter-finals.
Winners in 2021, Dortmund have now been eliminated in the last 16 in five of the past seven years.
Stuttgart’s win came shortly after five-time German Cup winners Frankfurt were dumped out away at Saarbruecken, conceding second-half goals to Kai Bruenker and Luca Kerber.
A “mega proud” Saarbruecken coach Ruediger Ziehl said “that’s just crazy”, while Bruenker told Sky Germany “tonight I’ll enjoy a beer and we’ll celebrate like beasts.”
Frankfurt debutant Noel Futkeu was sent off late on for lashing out at defender Marcel Gaus just six minutes after coming on as a substitute.
Saarbruecken, who are 11th in the third division, beat Bayern 2-1 at home in the second round last month.
They join Bayer Leverkusen in the quarter-finals after the Bundesliga leaders won 3-1 at home over second-tier Paderborn.
Despite having two goals ruled out for offside, Leverkusen eased past Paderborn thanks to strikes from Victor Boniface, Exequiel Palacios and Patrik Schick. Sebastian Klaas pulled one back late for the visitors.
Fortuna Duesseldorf, Borussia Moenchengladbach, St Pauli and Kaiserslautern all reached the last eight on Tuesday.
AFP