As he performed the song, images of the war, the Ukrainian flag and President Volodymyr Zelensky were shown on the screen behind him.
The audience responded with a chorus of loud boos and whistles, according to several media reports.
The Maggie May singer has previously been vocal in his support for Ukraine and reportedly rented a house for Ukrainian refugees in Britain.
According to German media, Stewart’s support for Ukraine had been well received at previous concerts in Copenhagen and Amsterdam.
Michael Roth, a foreign policy expert for German Chancellor Olaf Scholz’s SPD, on Sunday called Stewart the “hero of the day”.
“Thanks for your solidarity with the Ukrainian people!” he wrote on X, formerly Twitter.
But public opinion remains split on the issue, with some fearing Germany’s backing for Kyiv could risk escalating the war while others resent the amount of money being spent on Ukraine.
German far-left and far-right parties that are opposed to the government’s backing for Ukraine both scored major gains in last week’s European Union elections.