The 30-year-old actor quickly escorted her off stage and asked for security.
"She said something to Colin Farrell that no one heard, then he took her by the elbow, led her off stage, asked the cameramen to turn off their cameras and asked for security," said Molly Mattaini, who was visiting from St. Paul, Minn.
"Tonight Show" spokeswoman Tracy St. Pierre said the incident won't be broadcast.
The woman was detained by a Burbank police officer hired by NBC to provide security, but was not arrested "at the request of NBC," said police Sgt. Carlos Gomez.
Farrell's publicist did not immediately return messages left after business hours.
Mattaini, 16, said Farrell returned to the stage and apologized to the audience.
"He sat back down and said, 'My first stalker,' and Jay Leno said, 'Welcome to celebrity,"' Mattaini said.
Farrell remained on stage the rest of the show, appearing "very calm, very collected," Mattaini said. Later in the evening, he appeared at the premiere of his new movie, "Miami Vice."