Our new silicon masters asserted their power Wednesday, shutting down the world’s best-known stock exchange, grounding the planes of the world’s biggest airline, and crashing the website of the country’s most widely read financial news organization.

By the end of the day, the New York Stock Exchange, United Airlines and the Wall Street Journal were all up and running again, but the fallout from the computer glitches, system overloads and stressed back-up systems raised fresh questions about the strength on the nation’s cyber infrastructure and the heavy reliance on fallible technical systems.

“It was a bad day,” Thomas Farley, president of the New York Stock Exchange, admitted.

The Wall Street Journal crash was apparently the result of huge numbers of users turning to the website to track the problems of United and the New York Stock Exchange.

But the cascade of computer crashes sparked fresh concern in Washington, with President Obama getting a personal briefing on the NYSE trading halt and Securities and Exchange Committee Chair Mary Jo White said she was “closely monitoring” the situation.

The FBI and Department of Homeland Security checked into — and rejected — rumors that the failures were the result of a cyberattack by outside hackers.

Homeland Security Secretary Jeh Johnson said the problems at the stock exchange and United Airlines — which was forced to ground flights across the country Wednesday morning over what a spokesman called a “router issue” — were not the result of “nefarious” activity.

“I have spoken to the CEO of United, Jeff Smisek, myself. It appears from what we know at this stage that the malfunctions at United and the stock exchange were not the result of any nefarious actor,” Mr. Johnson said in a response to a question at a previously scheduled appearance at the Center for International and Strategic Studies in Washington.

The White House and the Justice Department said they had found no link between the United and NYSE incidents, nor was there any evidence at first blush of an attack by hackers.

“At this point, there is no indication malicious actors were involved in these technology issues,” White House press secretary Josh Earnest told reporters.

Mr. Farley was being interviewed on CNBC in the middle of a nearly four-hour trading halt on Wall Street. The New York Stock Exchange, the primary trading base for U.S. corporate giants from Apple and Google to General Motors and General Electric, was able to resume trading about 50 minutes before the traditional 4 p.m. trading close.

Officials at the NASDAQ said trading on its markets was proceeding normally, and trades on other U.S. markets appeared to be functioning normally. Mr. Farley noted that NYSE-issued stocks were also trading normally in other markets.

Analysts and traders said the bigger question for the stock market going ahead is not that there are occasional computer failures, but that back-up systems and redundant networks failed miserably when the primary system went down.

“There’s no excuse for this amount of time [to be down] in today’s markets,” one trader said.

The stock market’s computer problems came just hours after United Airways had to ground all of its flights for several hours over another computer malfunction. United officials said an “issue with a router” caused the operational disruptions, and that it would take much of Wednesday to catch up for the delayed and cancelled flights.

“The problem is humans can’t keep up with all the technology they have created,” said Avivah Litan, an analyst at Gartner, told the Associated Press. “It’s becoming unmanageable by the human brain. Our best hope may be that computers eventually will become smart enough to maintain themselves.”

To add financial insult to technological injury, U.S. markets staggered through another dreary day even when all the trades were going through, as worries about China and Greece sent values down on all the major exchanges.

By the end of the day, the Standard & Poor’s 500 index fell 34.66 points, or 1.7 percent, to close at 2,046.68.

The Dow Jones industrial average dipped 261.49 points, or 1.5 percent, to 17,515.42 and the Nasdaq slid 87.70 points, or 1.8 percent, to 4,909.76.

⦁ Benjamin Wolfgang and Brennan Weiss contributed to this article, which was based in part on wire service reports.

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