Nahid Hattar was hit by three bullets outside the court in the capital Amman where he was standing trial.
Police have arrested the suspected shooter, Riad Abdullah. Jordanian media said he was local imam who had been upset by the cartoon.
But security sources told the Jordan Times he was a known extremist.
A witness told the Associate Press news agency that Mr Abdullah had a long beard and was wearing a long robe, common among conservative Muslims.
