No flights were allowed to take off from 15:54 EST (19:54 GMT). It was the longest such suspension since the 11 September 2001 attacks, and the disruption was expected to last for days.
On Saturday, L3Harris said it had completed over 70% of the work to modernize communications infrastructure before the shutdown.
Duffy told a news conference that a router being worked on started flooding other air traffic control systems and created communication problems with planes. The government shut the airspace for safety, he said.
The maintenance, a switch from copper wire to fiber, was being carried out by contractor L3Harris, a technology company, Duffy said.
A nationwide ground stop has been ordered only one other time since all flights were banned from takeoff for several days after the 2001 attacks.
Some international flights were allowed to depart US airports, in an apparent effort to clear space.
L3Harris said it took the stop and its effects on passengers and airlines seriously."L3Harris takes the nationwide ground stop and its impact on travellers, airlines and air traffic operations seriously,"the company said.
Duffy warned that a similar issue could arise again unless Congress approved upgrades to air traffic control infrastructure.
President Donald Trump has requested $30.1 billion for the upgrades.