Dortmund said its team had a record of combating racism including organising trips to former Nazi concentration camps.
Lokomotive Leipzig also condemned the stickers in a statement, saying they had “nothing to do” with the team.
But public outrage has been muted compared to Italy and the German authorities have yet to make a move against the clubs.
The incidents occurred as the country’s rail operator Deutsche Bahn announced they would name a high-speed train after Anne Frank, leading to questions of just how far German society has tackled the issue of antisemitism.
In Italy, after antisemitic photos emerged of Anne Frank in a Roma FC jersey last week, authorities reacted forcefully to what has been seen as a step too far.
Hard-core fans of rival club Lazio admitted responsibility for the stickers but said they were surprised they attracted a big media outrage. Indeed, Antisemitic abuse is routinely used by Italian hooligans, particularly Lazio’s.
Sports Minister Luca Lotti ordered that a passage from “The Diary of Anne Frank” was read before matches last week, and Lazio’s President, Claudio Lotito, promised he would personally take 200 of his fans on an educational trip to Auschwitz every year from now on.
But Mr Lotito hit the headlines again when he was caught in a private conversation leaked to the local press describing his apologetic trip to Rome’s synagogue with a wreath of flowers as “a charade”.
The wreath was hurled into the Tiber by angry members of the community.
Most Jews in Rome dismissed the moves as “symbolic gestures”, and said tough measures are needed to fight antisemitism in Italian soccer.
“It wasn’t genuine”, said Daniele Regard, a 31-year-old Italian Jew from the capital who works as a press officer for Nicola Zingaretti, the president of Italy's Lazio region.
“Since going to matches as children, all Jewish football fans across the country are used to some degree of antisemitic abuse,” said Enrico Camp, a Roma supporter.
“In Rome, Lazio fans as well as those of Roma regularly chant the word ‘Jew’ as an insult against supporters. Racism is just not taken very seriously, even when scandals like this erupt, everything just goes back to normal after a week or so of outrage”.
Mr Lotito is likely to be sanctioned by Italian football authorities for allowing hooligans into Lazio’s stadium after circumvented an earlier ban for booing black players on the field.
The club’s head of communications Arturo Diaconale wrote in an editorial in L’Opinione that public outrage was a “storm of politically correct McCarthyism” and complained of “reverse racism” against Lazio.
It is still unclear whether Mr Lotito and Mr Diaconale will actually be taking their supporters to Auschwitz. Lazio did not respond to the JC’s requests for more details about the trip.
