All the airports involved are now back online, according to CBP, though some are still experiencing effects from the outage.
Photos posted on social networks by stranded passengers showed long lines at New York's JFK and Atlanta's Hartsfield-Jackson.
A passenger jet takes off from San Diego International Airport. All airports were back on line after wait times for travelers that were longer than usual, it said.
All airports are back on line after a temporary outage of #CBP's processing systems.
Season's worst fog at IGI, over 200 flights hit
Sources said that almost 50 planes were sent to nearby airports as many pilots were not trained in this technology. Take-offs at IGI require a minimum RVR of 125 metres and landings can take place with a minimum RVR of 50 metres.
Several airports Tweeted out warnings to passengers, like this one, from Dallas-Fort Worth: "Good evening, there is a system issue affecting processing times for customs".
For roughly two hours, the customs computer systems were unable to recognize who was a US citizen, a resident or a visitor, so everyone had to go through an immigration officer, making the process much longer.
"The machines for customs and border patrol aren't working, so all the things are printing out with X's on them and everyone's freaking out, so the lines about an hour to get thru", said Brittany Jason. "CBP officers continued to process worldwide travellers using alternative procedures at affected airports. It's all over the place".
The agency said it had access to the national security-related databases during the outage. No indication the disruption was malicious in nature.