Wolfsburg produced the first shock of this season's German Cup, knocking out holders RB Leipzig with an inspired 1-0 win as fourth-tier Homburg upset Greuther Fuerth and Kaiserslautern sank Cologne.
The Red Bull outfit have a rich recent pedigree in the competition, reaching the previous three finals, losing in 2021 to Borussia Dortmund first but winning the last two against Freiburg and Frankfurt.
However, Wolfsburg have not made it beyond the quarter-finals since lifting the trophy in 2015.
But on home turf, Kovac's side put their Bundesliga troubles behind them and pulled off their biggest victory of the season.
Despite going into this game having lost four of their last five league games, Wolfsburg flew out of the blocks.
Summer signing Cerny latched onto a perfectly-weighted pass by Tiago Tomas and unleashed an unstoppable left-footed drive into the roof of the net for his first goal of the season.
Leipzig struggled to find their rhythm and when Yussuf Poulsen saw red nine minutes into the second half for a clumsy second yellow, the reigning champions' chances disappeared.
In another surprise result, Greuther Fuerth of Germany's second division were beaten 2-1 at home by fourth tier Homburg with Phil Harres scoring a late winner.
Bundesliga strugglers Cologne were sent packing by second-tier Kaiserslautern, whose slick performance put them 3-0 up after 65 minutes and seemingly out of sight.
Cologne have now won only one of their last 10 games.
In an extraordinary game between third division Unterhaching and second-tier Fortuna Duesseldorf, the underdogs were pegged back to 3-3 after being 2-0 up, with Duesseldorf eventually prevailing 6-3 after extra time.
Hamburg were 13 minutes from going out to third-tier Arminia Bielefeld but levelled the game at 1-1, with the second division club eventually clinching victory 4-3 in a penalty shoot-out.
Union Berlin qualified for the Champions League for the first time in their history last season, but their domestic form this term has been poor.
The only goal of the game came in first half stoppage time courtesy of Deniz Undav.
Borussia Moenchengladbach, three-time German Cup winners, beat Heidenheim 3-1 to reach the last 16, while Johannes Eggestein scored a 102nd minute winner for St. Pauli, who needed extra time to beat Schalke 2-1.