Andrew Meyer was questioning Senator Kerry on why he did not contest the results of the 2004 election.
University officials said he exceeded his allotted time and became disruptive after his microphone was cut off.
Video footage shows police pulling Mr Meyer from the audience and pinning him to the ground before stunning him.
The 21-year-old student can be heard screaming for help as the stun gun is administered.
Mr Meyer was arrested and charged with resisting an officer with violence and disturbing the peace, reports local newspaper the Gainesville Sun.
After spending the night in Alachua County jail, he was released on Tuesday morning, the Gainesville Sun reports.
A spokesman for the university, Steve Orlando, said campus police would conduct an internal investigation into whether the weapon had been used appropriately.