The boy, 17, shocked passengers on board the Copa Airlines flight from Panama City as he flung the door open before leaping out on Tuesday.
He was confronted by construction staff working nearby and held until police arrived to arrest him.
The boy, a US citizen, was not harmed.
Passengers said the teenager seemed fidgety and anxious throughout the flight and that he had acted very quickly, making it difficult to stop him, according to the Associated Press news agency.
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One eyewitness, Sophia Gibson, told San Jose's KNTV that people were shocked when the passenger leapt through the door and onto the plane's wing.
"It was as if he was like flying out, like it was really fast," Ms Gibson said.
Another passenger, 11-year-old Andrea Sepulveda Guzman, told CBS San Francisco that people had started to scream.
"This guy, I see him jump on the wing and then he starts climbing down the wing and then he just runs. And then he just starts running the other way. And everyone was just screaming," she said.
It was not immediately clear why the teenager had leapt from the plane and run.
San Francisco Airport spokesman Doug Yakel said the boy was travelling alone, adding that no runways or flights were affected by the incident.
A Copa Airlines Flight 208 crew member closed the emergency door and the plane taxied to its gate, where all remaining passengers alighted without incident, the Panama-based airline said in a statement on Tuesday.
The airline added that an investigation was under way and that it was co-operating with the authorities.

The Westgate development in the city centre will eventually have more than 100 shops, 25 restaurants and cafes, a cinema and 61 flats.
The multi-storey car park on the site was demolished last year. It will be replaced with a 1,000-space underground car park.
The development is due for completion in autumn next year.
It will include rooftop terrace dining and new public spaces.
Site owner Westgate Oxford Alliance, a joint venture between commercial property company Land Securities and The Crown Estate, said the development would cover 800,000 sq ft (74,322 sq m) when complete.
Preparatory work began in February 2015 following planning approval by Oxford City Council.

The X-47B jet is being designed by weapons manufacturer Northrop Grumman for the US Navy.
It was in the air for 29 minutes during its maiden flight and reached an altitude of 5,000 feet.
Officials say it will help form part of a new generation of unmanned drones and works like a smaller version of the B-2 Stealth Bomber.
As such it would be very different from the current fleet of remote controlled military planes like the Predator and Reaper.
Instead the X-47B would be virtually invisible to radar and fly at much faster speeds than those older, propeller driven machines.
In a statement Captain Jaime Engdahl, a programme manager for the warplane, said: "Today we got a glimpse towards the future as the Navy's first-ever tailless, jet-powered unmanned aircraft took to the skies."
The flight was primarily designed to test the jet's guidance and navigation systems and the aerodynamic control of the tailless design.
It was controlled from the ground by a joint team of the company's engineers and Navy specialists.
Northrop is building the bomber as part of a Â£395 million contract signed in 2007.
Janis Pamiljans is vice-president of Northrop Grumman's Aerospace Systems sector.
"Designing a tailless, fighter-sized unmanned aircraft from a clean sheet is no small feat.
"Commitment, collaboration and uncompromising technical excellence among the Navy [and] Northrop Grumman made today's flight a reality.
"We are indeed honoured to have given wings to the Navy's vision for exploring unmanned carrier aviation."
Although it will be several years before the X-47B is ready for operations officials say it should have its first test flight from an aircraft carrier in 2013.
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A teenager has been detained after opening the emergency door of a passenger plane and sliding down a wing onto the tarmac minutes after touching down in San Francisco, officials say.
[NEXT_CONCEPT]
Work has begun to demolish a 1970s shopping centre in the centre of Oxford as part of a £440m redevelopment.
[NEXT_CONCEPT]
Military chiefs in America say a new, unmanned stealth bomber has carried out its first test flight.