The argument escalated into a physical altercation and one man stabbed the other with a pen. Authorities said the victim was taken to a local hospital with a minor cut near his eyelid.
The suspect was arrested on suspicion of assault with a deadly weapon.
The men were in their early 20s and the pen stabbing occurred between panels for "Resident Evil: Afterlife" and two upcoming films from Universal Studios, "Paul" and "Cowboys and Aliens," which was delayed for 45 minutes because of the incident.
Comic-Con is San Diego's largest annual convention.
CNS contributed to this report.