Captain Schmelzer was not only dropped from the starting XI but left out of Dortmund's matchday squad for the Bundesliga fixture at Signal Iduna Park on Saturday.
Stoger instead started Manuel Akanji at left-back, while Julian Weigl, Mario Gotze and Jadon Sancho were also drafted into the team following last weekend's 2-0 derby defeat to Schalke.
The changes worked too, with Dortmund running out convincing winners to close in on a top-four finish that will secure Champions League football for next season.
"It's a sporting decision," Stoger told Sky when asked about Schmelzer's absence prior to kick-off.
"A captain usually plays in the starting line-up. Like several other players, he has not delivered optimal performances over the course of recent weeks.
"We need a certain degree of robustness in the full-back positions to counter the quick lads in the Leverkusen team."
Schmelzer was in the crowd to witness Marco Reus score twice for Dortmund, who have leapfrogged Leverkusen to move into third place in the table.
Sancho also scored his maiden goal for the club, the Englishman breaking the deadlock before going on to provide two assists in his first league start since January.