The 24-year-old player was randomly selected for a secondary screening at Terminal 1 and became uncooperative with the process, airport police Sgt. Karla Ortiz said. She said he told a TSA agent that he had a bomb before walking to the gate. When airport police officers caught up with him, Ortiz said Smith became uncooperative and was taken into custody.
He was booked for investigation of making a false bomb threat, Ortiz said.
A message seeking comment from Smith's agent wasn't immediately returned.
With the arrest, Smith is involved in three pending criminal cases.
"We are disappointed to learn of the incident today involving Aldon Smith," 49ers general manager Trent Baalke said in a statement. "As this is a pending legal matter and we are still gathering the pertinent facts, we will have no further comment."
A fearsome pass-rushing specialist, Smith took a five-game leave of absence from the 49ers last season to undergo treatment for substance abuse. He rejoined the team Nov. 5.
Smith played in a 27-7 home loss to the Indianapolis Colts on Sept. 22, two days after he was arrested and jailed on suspicion of DUI and marijuana possession. After the game, he publicly apologized for his behavior and later announced he would leave for treatment.
Leading up to the playoffs in early January, Smith said during an interview with The Associated Press he was encouraged by the strides he had made to better himself off the football field that put life - and his work - in perspective. He said at the time he hadn't had any alcohol since before his Sept. 20 DUI arrest, and that he wasn't craving it. When he rejoined the team Nov. 5, he insisted he was on the path to lifelong sobriety stuck by that statement.
His teammates rallied around him in support of his rehab and, later, his return to the team.
Smith emerged as one of the NFL's most-feared pass rushers in 2012. He had a franchise-record 19.5 sacks that year, but failed to record a sack in his final six games including the team's postseason Super Bowl run.
Smith finished with 8½ sacks and 34 tackles in 11 games last season, making eight starts.
In November, Smith pleaded not guilty to three felony counts of illegal possession of an assault weapon, stemming from a June 2012 party at his home. Investigators say several shots were fired, two partygoers were injured and Smith was stabbed. In the subsequent investigation, prosecutors say detectives found five unregistered weapons in Smith's house, including two Bushmaster rifles and an Armalite AR-10T. They say those are assault weapons illegal to possess under California law.
Smith and former teammate Delanie Walker were named in a lawsuit last September filed in Santa Clara County Superior Court by a Northern California man who said he was shot at a party at Smith's house on June 29, 2012. The players charged a $10 admission and $5 per drink, the lawsuit said. Smith and now-Tennessee Titans tight end Walker were allegedly intoxicated on Smith's balcony when they fired gunshots in the air while trying to end the party, the lawsuit said.
Smith, selected seventh overall in the 2011 draft out of Missouri, had previously been arrested on suspicion of DUI in January 2012 in Miami shortly after the 49ers lost in the NFC championship game.
This is the latest in a long list of legal issues for 49ers players the past two years - and recently, too. The Niners, who lost to the rival and eventual champion Seattle Seahawks in the NFC championship game, have made nearly as much news away from the field as they have in free agency this offseason.
On Thursday, 49ers quarterback Colin Kaepernick was one of three NFL players named in a Miami police report involving a woman who passed out in a hotel and later woke up in a hospital not knowing how she got there, though no one has been charged with a crime. Kaepernick, 49ers wide receiver Quinton Patton and Seahawks wide receiver Ricardo Lockette - a former 49er - were with the woman at a Miami hotel where Lockette lives, according to the Miami Police Department report. The police say it's too early to determine whether a crime was committed.
Late last month in San Jose, 49ers cornerback Chris Culliver was arrested on suspicion of felony hit and run and reckless driving after he drove a car into a bicyclist and fled. He is the player who underwent sensitivity training after his anti-gay remarks leading up to the Super Bowl after the 2012 season. He has done outreach to the lesbian, gay, bisexual and transgender community.
Last summer, another starting linebacker, Ahmad Brooks, was investigated by the Santa Clara County District Attorney's office on allegations that Brooks repeatedly hit a teammate on the head with a beer bottle. No assault charges were filed because of insufficient evidence.
According to police, Brooks hit then-teammate Lamar Divens with the bottle three times and then punched him in the face during an early morning argument June 8. Divens sustained a 3-inch cut on his forehead.
Another member of the defense, Demarcus Dobbs, was suspended for Week 1 last season for his own arrest on suspicion of DUI and marijuana possession in 2012.