The Dortmund boss says his side were forced to pay for their own profligacy after the Bundesliga champions struck three times in the second half
The Bavarians claimed their first Bundesliga victory over BVB since February 2010 on Saturday, scoring three late goals through Mario Gotze, Arjen Robben and Thomas Muller to go seven points clear of their rivals.
However, Klopp feels that his side, who had missed a number of chances earlier in the clash, did not deserve to lose by such a heavy margin.
"I do not care how badly we lost. The second and the third goal do not represent this match," he told Sky after the match.
"Bayern played differently. They played many long balls and they were very patient. We had the bigger chances until the 1-0 and we had a huge chance for the 1-1.
"But you have to convert these chances. After the second goal you could see the team had a crack. I don't care about the third goal."
Meanwhile, BVB goalkeeper and stand-in captain Roman Weidenfeller was adamant that his side were the better of the two teams over the course of the 90 minutes.
"We were better in this game, but matches are decided by goals. And at the moment we are not able to score the decisive goals," he said.
"We lack determination in front of the goal. Sometimes you just have to shoot and score. The heavy loss was not deserved. We opened up to try to get a 1-1 draw.
"It does not matter how much we lost by. It is just bitter that we did not reward ourselves."