The cause of the problem was not immediately disclosed, but the exchange quickly ruled out a cyberattack.
Problems began during the morning and at 11:32am EDT the NYSE halted all trading to prevent the effects of the "internal technical issue" from affecting the overall market.
"NYSE has temporarily suspended trading in all symbols," the market said in a message to traders. "All open orders will be cancelled."
Updates for the public were few and far between during the duration of the outage, although the NYSE was said to be in constant contact with the Treasury Department and the Securities and Exchange Commission.
The problems even reached the desk of President Obama. He was briefed by Homeland Security Advisor Lisa Monaco, who told him there was no sign that malicious actors were to blame.
Trading of most stocks resumed at 3:10pm EDT and no further problems were reported.
The disruption was the second of the day for the exchange.
Earlier in the trading session, connectivity to three of the NYSE's connection points for computerized trading were hit by a fault that caused trading in about 200 stocks to be halted. Two of the affected gateways were returned to service and one was planned to be restored at the end of the Wednesday session.
Also the same day, United Airlines was forced to ground hundreds of flights at the inconvenience of thousands of travelers due to a computer glitch. Few details were released by the airline, but the problem is understood to have been related to a network router.
Martyn Williams covers mobile telecoms, Silicon Valley and general technology breaking news for The IDG News Service. Follow Martyn on Twitter at @martyn_williams. Martyn's e-mail address is martyn_williams@idg.com