Dortmund suffered a 2-1 aggregate loss in the last 16 after being held to a 0-0 draw in the second leg at Red Bull Arena.
Stoger said his team were unable to deliver what they wanted away from home as they made a surprise exit.
"In the first half we showed nearly nothing of what we planned to do," he told a news conference.
"There are different ways in football to get successful and create chances, the quality of your football included. We thought we had enough of that [quality] on the pitch in the first half, but we saw nothing of it.
"Concerning the areas and spaces we wanted to use, also in the box for crosses, we did nothing. That's disappointing for us.
"The pitch was not the best, but we made it partially hard for ourselves. Nevertheless, we saw that we can create chances with a little more courage in the second half.
"At the end of the day, Salzburg probably deserved the next round over the two games. We had to congratulate them and I want to compliment my compatriots."