Merkel leapt from her seat along with 80,000 other fans as the defending champions returned to winning ways after a 1-1 draw at Nuremberg with a display of the kind of football which has earned them the Bundesliga title two years running.
Klopp could understand Merkel's enthusiasm for his side's goals in the 3-0 win, but denied that they have a new fan.
"The Germans don't have to worry about that - she is just a fan of beautiful football," said Klopp afterwards.
"If she wants, she is more than welcome to come every fortnight."
Merkel was not the only person taken aback by the quality of Dortmund's play at the Westfalenstadion.
"It was an incredibly good performance from my team," said Klopp to Sky television.
"Over the 90 minutes, we often did even more than the necessary, but we never did less than necessary.
"That was so strong."
Even Bayer Leverkusen's joint coach Sascha Lewandowski acknowledged his side have a long way to go before they can match their Westphalian neighbours.
"Dortmund do things automatically in many areas whereas we are just starting to resolve things quicker and better," he said.
"You have got to expect that, and that is why you can come off worse, but we were completely passive right from the first minute and that is what really bothers us."