The cartoon, which won a national prize in 2015, shows a decapitated figure labelled "Charlie Hebdo" sticking its tongue out at a bearded man with a bloody sword.
The attack took place in front of a building where Islamist militants gunned down employees of Charlie Hebdo in 2015 because of the republication of cartoons depicting Prophet Mohammad.
The January 2015 attacks in Paris, where no less than 17 people lost their lives, were claimed by the Islamic state.
Original plans for the contest were shelved over a year ago for fear of violent retribution.
The Respekt project started in 2011 with artists in Russia and the German Goethe-Institut in Moscow.
The cartoonist responsible for the drawing replaced the initial illustration with one that appears to be a sequel rather than an entirely different scenario.
Wilders denies that he intended to provoke, claiming that he did it "because we have to show that we stand for freedom of speech and that we will never surrender to violence."
"Every print-run was torture because the others are no longer there," says Renald Luzier
The controversy started when Yisrael Beytenu planned to give out copies of French newspaper Charlie Hebdo’s "survivors’ issue."