Leon Goretzka had a 51st-minute strike ruled out in Saturday's goalless draw with RB Leipzig after Robert Lewandowski was adjudged to be marginally offside.
Bayern president Uli Hoeness described the decision to disallow the goal as the "joke of the year" but Kovac, although casting doubt on using technology to intervene for such tight calls, has defended the system.
"I have always said that I am a friend of VAR," he said.
"As it turned out, it was probably a very slight offside. For me, the only question in these situations is: when is the stop button pressed? If I do it too late, then it can be offside and if I press too early, then it is not offside.
"I think you have to hit this point to one hundredth of a second exactly and I don't know if that's possible. But it was offside, and I don't want to discuss that at all."
The leaders face Eintracht Frankfurt at the Allianz Arena next Saturday, while Dortmund travel to Borussia Monchengladbach at the same time, and Kovac hopes Bayern can now get the job done against his former employers.
"We have the chance to become champions next week with a point or a victory," he said. "Life writes the best stories. I can play against my old club and can try to win the championship.
Bayern CEO Karl-Heinz Rummenigge confirmed Thiago Alcantara bruised his knee in Bayern's stalemate with Leipzig, but he is expected to be available for the final day of the season.