Bayern suffered a 2-1 home loss in their Champions League quarter-final first leg on Tuesday, with the return leg next week in Milan.
Kovac, whose team lost 4-0 to Barcelona on Wednesday in their quarter-final to all but end their Champions League run, said Bayern could be distracted by their return leg in Italy and their better chances of advancing.
"Bayern have a tough task ahead of them in Milan, to turn the tie," Kovac told a press conference. "In their heads, they may be a bit in Milan, and we will have to take advantage of that in Munich.
"But that can happen only if we are at 100%. If we put in less than 100%, it is difficult to decide the game in our favour."
Bayern are in top spot on 68 points, six clear of second-placed Bayer Leverkusen, while Dortmund are eighth on 41, five off fourth spot that leads to automatic Champions League qualification.
Kovac said his team needed to be far sharper than against Barcelona if they wanted to have any chance in Munich.
"When you play football, you have to work collectively and we did not do that against Barcelona," he added.
"That is what I addressed and what we need to change for tomorrow's game because Bayern also have world-class players. If we don't do that, it will be tough in Munich, this is what I demand and I will demand it tomorrow as well."