Leverkusen win pleases Klopp
Bayern, who won their opening eight matches, were stunned 2-1 at home on Saturday, while Dortmund accounted for Freiburg 2-0.
Despite the loss, Bayern remain on top of the table with 24 points, nine points ahead of Dortmund in fourth.
Klopp said he was pleased for Leverkusen, who ironically moved equal on points with Dortmund following the win.
"I'm happy for Leverkusen," he said.
"But in the second half Bayern Munich showed a slightly stronger performance than Bayer, let's put it that way."
Sidney Sam scored the decisive goal in the 87th minute, after Bayern forward Mario Mandzukic had cancelled out Stefan Kiessling's opener.
"After the 1-1 in the middle of the second half I didn't expect Leverkusen to come back," Klopp said.
"But that's football. Bayern was lacking some precision when it came to converting their opportunities. Apart from that they were much better.
"I didn't expect Bayern to win every game this season though."