Smith was booked Sunday afternoon, according to LAPD Sgt. Michael Fox. Smith was charged with a false bomb report, which is punishable by up to one year in jail. He posted $20,000 bail Sunday night, according to multiple reports.
49ers general manager Trent Baalke issued a statement saying: "We are disappointed to learn of the incident today involving Aldon Smith. As this is a pending legal matter and we are still gathering the pertinent facts, we will have no further comment."
According to Los Angeles World Airports PIO Sgt. Karla Ortiz, the incident happened as the man, later identified as Smith, was going through Terminal 1 screening and was randomly selected for secondary screening.
Smith then became belligerent and uncooperative with the process and with the TSA agent, making a comment indicating that he was in possession of a bomb before proceeding toward the gate area, according to Ortiz.
Los Angeles Airport Police made contact with him at the gate and he then became uncooperative again and was detained and taken into custody by Airport Police.
Many people on the scene, including former Marine veteran Clayton Mullaly, captured the incident on video.
This incident is Smith's latest run-in with the law.
In November, Smith pleaded not guilty to three felony counts of illegal possession of an assault weapon, stemming from an incident at a party at his home in 2012.
Smith also missed five games this past season while spending time in an alcohol treatment center. He entered treatment voluntarily three days after he was arrested for drunken driving for the second time since early 2012.
Despite the five-game absence, Smith finished with 12 sacks and 34 tackles over the course of the Niners' season, which ended in a NFC Championship Game loss to division rival Seattle.
Smith, 24, is facing charges for both the arrest for the incident at his home and the September arrest for drunk driving. This latest incident could trigger league discipline. The NFL did not suspend Smith after the September arrest. In October, commissioner Roger Goodell said the fact that Smith voluntarily sought treatment could play a role in him not getting a suspension.
Information from ESPN.com's 49ers reporter Bill Williamson and The Associated Press was used in this report.