A nationwide ground stop ended around 8:15 pm ET, and some domestic flights have now departed from US airports.
However, normalizing air traffic after the longest flight stoppage in 25 years will be slow, authorities warned.
Officials say the system is likely to be operating normally in time to handle the Thanksgiving travel rush.
Here's what to know.
Flights have resumed but disruption continues
The Federal Aviation Administration said airplane departures could resume late Friday evening Eastern time. Passengers should contact their airlines for information about their flights, the FAA said.
The ripple effect from the stoppage could be felt for days, however.
More than 2,500 flights were canceled in the US on Saturday and hundreds more were delayed, according to FlightAware, a website that tracks flight disruptions.
Transportation Secretary Sean Duffy warned Americans traveling that getting air traffic back to normal won't be quick.
International flights are being handled on a case-by-case basis, according to Homeland Security Secretary Markwayne Mullin.
San Francisco airport said that flights headed across the Pacific Ocean were cleared to leave the airport from Friday evening. That included flights destined for Hawaii and Asia.
Europe's aviation agency suspended U.S.-bound departures at the request of the FAA from 5 p.m. Eastern on Friday until midnight.
Airlines are obligated to offer free rebooking on another flight for travelers who want to continue their journey, or a refund if their flight was canceled and they decide not to take the trip.
The reason for the grounding
New technology being hooked up to the nation's air traffic control system overloaded antiquated equipment, Trump administration officials said.
That caused "intermittent" communications and radar gaps, leading to the flight shutdown of more than four hours, according to officials.
Duffy suggested more disruptions might occur.
"We didn't think we would have this kind of outage. We did," he said.
The air traffic control modernization began last year after Congress approved $12.5 billion of funding. Duffy and the White House are pushing for $30 billion more to complete the work.
The Microsoft outage and cyberattacks were unrelated to the stoppage
Microsoft said it had no indication that the ground stop was related to the service disruption that took Outlook and other services offline Thursday, a spokesperson for the company said.
Mullin said there is no indication the failure was related to a cyberattack, either.
"There was never any lives at risk," Mullin added. "There was no flights at risk. FAA was able to handle it. We did it."
The ground stop was enacted "out of an abundance of caution," he said.