The attacker, identified as Ved Prakash, was detained by police, which quizzed him.
He talked about alleged irregularities in distribution of CNG stickers and claimed that no action has been taken though a complaint was filed by him with the Chief Minister.
The incident happened during a press conference at Delhi Secretariat here addressed by Kejriwal on roll out of the second phase of the Odd-Even scheme from April 15.
The shoe fell short of the Chief Minister, who had earlier been targeted with ink and was slapped by a man during campaigning for last assembly election.
The attacker, who is about 26-27 years of age, shouted as he was being whisked away. Kejriwal later continued with the press conference.