The processing system outage began at about 7.30pm EST (0030 GMT) and was resolved about 9.30pm EST (0230 GMT), the Customs agency said in a statement.
All airports were back on line after wait times for travellers that were longer than usual, it said.
"At this time, there is no indication the service disruption was malicious in nature," the agency said. It gave no explanation for the disruption and said travellers were processed using alternative procedures.
Travellers entering the United States from overseas posted photos on social media of long lines at John F. Kennedy International Airport in New York and at Hartsfield-Jackson Atlanta International Airport.
“No one has been getting past JFK Airport immigration for the last hour. Line is a few 100 deep. Seems like their system did completely go down. Happy New Year!” said Jessica Yang, a program manager at Microsoft, in a Twitter post.
“Operations returning to normal as @CustomsBorder computer issue resolved. Issue affected other US airports. Thanks for your patience,” Miami International Airport said in a Twitter post, source from the Straits Times.