A search of the United Airlines terminal failed to find the man, and the terminal was reopened mid-morning, with all passengers being rescreened, said airport spokesman Ron Wilson.
"We've searched the terminal. It's safe and secure," Wilson said. "It's unfortunate that one individual can cause this madness."
About a quarter of the airport was evacuated around 7 a.m., the peak of the morning travel rush, after the residue was detected on the man's shoes at a checkpoint, said airport spokesman Mike McCarron. "When they went to stop him, he didn't stop," McCarron said.
The Federal Aviation Administration ordered U.S. airports to perform random shoe checks in late December after passenger Richard Reid, 28, allegedly attempted to set fire to a pair of explosive sneakers on an American Airlines flight traveling from Paris to Miami.
The explosive material could be anything from fireworks residue to nitroglycerin tablets, McCarron said. It was detected after a gauze-like material was wiped across the man's shoes, then put through a machine.
McCarron didn't know whether the residue was discovered in a random check or if the man raised suspicion. The passenger was described as a white male in his 40s. Airport officials were unsure if video cameras at the checkpoint captured the man's image.
The incident forced officials to hold all 27 outgoing flights from the area and affected at least 20 inbound flights, Wilson said.
San Francisco officials immediately ordered the boarding area cleared, shutting some 30 gates in the airport's Terminal 3 and delaying as many as 80 domestic flights of United Airlines, the airport's busiest carrier.
In addition, passengers who had already boarded a number of jets were told to get off and go through security screening procedures again.
CBS News Correspondent John Blackstone reports six planes took off from San Francisco before the incident was reported to the FAA. Two of those flights, one to New York and one to Washington, were diverted to Chicago and checked for bombs. Nothing was found.
At least 3,000 people were evacuated from the terminal, many of them left standing outside the building on an unusually cold San Francisco day, with temperatures in the 30s.
"No one's told us anything about what's going on, it's very frustrating," said Ethan McLaughlin of San Carlos, who was turned back while boarding his flight to Manchester, N.H., for a job interview.
Eva Renninger, returning to Santa Barbara from Kauai, Hawaii, said a little inconvenience was worth the extra safety.
"There's no point panicking. I would rather be here than on the plane that blows up," she said.
United spokesman Chris Brathwaite in Chicago said the airline's system was operating "qute well" nationally despite delays into and out of San Francisco, though further delays were possible because of snow across parts of the country.
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