Dortmund scored the only goal of the game in the 65th minute when Shinji Kagawa's deflected pass looped over Jerome Boateng and into the path of Mario Gotze, who showed quick reflexes to fire the ball past a stranded Manuel Neuer.
However, Bayern then spent the remainder of the match dictating possession, but failed to carve open a clear cut scoring opportunity despite much of the game being played out in their attacking third.
And Heynckes admits his side lacked invention against a stubborn Dortmund side, who had Mats Hummels to thank for some brave defending.
"When you play against Borussia Dortmund, you need to pose much more pressure than we have done today [Saturday]," Heynckes told Bundesliga.de.
"We have not understood how to increase the tempo and create scoring chances, until the final phase when he had two clear chances to score."
Heynckes also insisted his players had been unfortunate to concede, and felt they deserved a point from the game.
"The goal [Gotze scored] was very unfortunate, and in my view this was a typical 0-0 game."
Bayern's lead at the top of the table has now been reduced to just two points, with Dortmund just ahead of Borussia Monchengladbach in second place on goal difference.