The two countries are marking 55 years of diplomatic relations
The Foreign Minister also called on Germany to join the effort to stop the UN arms embargo from running out in October.
The flyover comes in the midst of a historic two-week joint military exercise between Israel and Germany.
The letter, published on the website of "Artists for Palestine UK," was signed by filmmaker Sivan and 13 other Israeli artists who called on people to boycott the event.
"Germany does not classify Hezbollah as a a terrorist organization, it may continue to collect donations and propaganda. That must have an end," said one German politician.
The same BDS supporters who interrupted the book reading have previously crashed a Holocaust survivor's speech. Author Arye Sharuz Shalicar had been speaking about antisemitism in Germany.
The US ambassador Richard Grenell suggested that the Bundestag resolution against BDS should apply to Iran's regime because it seeks the destruction of the Jewish state.
Rogel Rachman, an Israeli diplomat at the Berlin embassy, tweeted on Sunday: “Uwe Becker mayor of Frankfurt in the Israel Congress ‘Jerusalem is the capital of Israel.”’
A German-Israeli book story