No suspicious packages were found and passengers were being allowed back in the terminal buildings.
Earlier, flights were on hold after the airport received a "very specific threat" by phone at 14:00 (19:00 GMT).
Local news channel KENS 5 reported that one flight was diverted, three cancelled, and 28 delayed.
As the airport was reopened, officials warned there was heavy road traffic in the surrounding area.
While the airport was closed local news sources reported that dogs trained to detect bombs raised suspicions over three cars in an airport car park, indicating there could be explosives inside.
Airport officials confirmed that all three cars were eventually cleared.
Meanwhile, passengers were herded onto the runways, away from the airport buildings, before they were taken to a nearby high school while the search was under way.
About 2,000 passengers were cleared out of the airport during the evacuation, Fire Department spokeswoman Deborah Foster told the Associated Press.
The incident was brought to officials' attention at about 14:00, and the airport tweeted confirmation that it was evacuating the terminal buildings at 14:35.
San Antonio International Airport handles about 260 flights, carrying between 14,000 and 15,000 passengers each day, airport spokesman Rich Johnson said.
The spokesman said incoming planes landed they were directed away from the airport buildings.
Other planes were also asked to wait on runways, the spokesman said.
The international airport in San Antonio, Texas, has reopened several hours after it evacuated passengers and searched for an alleged bomb threat.