The outage on Monday night affected airports including New York's JFK, San Francisco and Denver, as global travellers arrived from holiday travels on New Year's Day, reports CNN.
The processing system outage began at about 7:30 p.m. EST (0030 GMT) and was resolved about 9:30 EST (0230 GMT), the customs agency said in a statement.
The department said it was still able to screen travellers using "national security-related databases".
CBP officers continued to process worldwide passengers using alternative procedures, but the agency acknowledged that travelers at some ports of entry experienced longer than usual wait times.
"CBP officers continued to process worldwide travellers using alternative procedures at affected airports".
Several airports, including JFK International and the Dallas Fort Worth International acknowledged the delays on Twitter.
Sky News Australia and USA media outlets are reporting global airport systems have failed across the country on one of the busiest evenings to travel in the states.
According to CNN, the temporary outage lasted two hours and affected global travelers passing through several major airports, including New York's John F. Kennedy worldwide. "Happy New Year!" said Jessica Yang, a programme manager at Microsoft, in a Twitter post.
Other airports, including Denver International Airport, also said they were affected. A similar outage had hit computer systems a year ago. The issue affected other USA airports.