Fans had taken part in a lengthy scavenger hunt for clues as to the whereabouts of a screening of new Marvel short film Item 47, set to be released on the upcoming Blu-ray of The Avengers.
According to The Hollywood Reporter, when fans gathered in the auditorium, the lights went down and Downey Jr appeared on screen, sat on a toilet and holding a microphone.
The actor joked: "I am coming to you live from a bathroom stall in Wilmington, North Carolina, where I am prepping to shoot the very famous toilet escape sequence from Iron Man 3.
"I'd like to congratulate you for being here, sitting where you are today, as am I, dropping a water moccasin."
The 47-year-old then introduced the short, which follows a young couple who discover the alien weapon left behind by the Chitauri at the end of The Avengers.
The Iron Man 3 panel is set to take place later today (July 14) at Comic-Con in San Diego. Downey Jr has told fans to expect an unpredictable third entry in the series, saying that he "doesn't know where they can go" after the upcoming film.
Watch the trailer for The Avengers below:
Photo gallery - Comic-Con 2012 stars: