The thickset man made a brief speech in Arabic during the question and answer session, defending US policy and accusing al-Zeidi of "working for dictatorship in Iraq," before throwing his shoe.
Al-Zeidi later quipped: "He stole my technique."
It was not clear if the intruder was a journalist or just pretended to be one to attend the news conference at a centre for foreign reporters.
Al-Zeidi's brother, Maithan, chased the attacker in the audience and pelted him with a shoe as he left the room.
Al-Zeidi became a hero among many opponents of the Iraq war when he threw his shoes at Bush during a news conference in Baghdad in December 2008.
"This is from the widows, the orphans and those who were killed in Iraq," he said as the shoes left his hand for Bush's face, who ducked and escaped unharmed.
Al-Zeidi was quickly wrestled to the ground by security guards, then imprisoned for nine months before being released in September.
The Paris news conference was held so he could talk about his experiences.
At his appearance in Paris, organised by the Arab Press Club, he said he is staying in Geneva for medical treatment for broken teeth, stomach complaints, fractures and torn back ligaments that he suffered.