Tuesday’s short-lived but violent squalls wreaked more than a bit of havoc in the region, shorting out traffic signals, felling trees and electrical wires, and snarling the Long Island Rail Road’s rush hour.

Suffolk police warned drivers to treat malfunctioning traffic lights as if they were stop signs.

A woman driving in Bellmore escaped injury but had to be rescued from her car by two Nassau officers after her vehicle was hit by a tree as well as downed power lines, police said.

“It was like a thunderous roar,” the driver Denise Giammarino said. “I look up . . . and I can see this giant tree on top of me.”

Wind gusts almost hit 50 miles per hour, according to the Upton-based National Weather Service.

The only good news?

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NWS meteorologist David Wally said the South Shore escaped the coastal flooding it had warned of on Monday because the high winds arrived later than expected, during a low-tide cycle.

The wind and rain accompanied the near-record-setting warm temperatures that were an extreme turnaround from the arctic air that mauled Long Island through the weekend.

Islip just missed setting a record by one degree, as the temperature hit 55 at 3:30 p.m. before beginning to retreat, said Wally.

However, temperatures were expected to drop overnight, with the thermometer falling to freezing, and Wally cautioned motorists to watch out for black ice in the morning.

Tuesday’s high winds were powered by that approaching cold front, and tapped strong winds that usually stay in higher altitudes, the NWS said. The higher winds that were driven earthward produced what Wally called “a real strong, low-level jet.”

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The result was a high of more than 16,000 customers without power by about 4:30 p.m., although that number came down steadily through the night, according to PSEG Long Island.

Two Long Island Rail Road branches bore the brunt of the delays — the Port Jefferson and Ronkonkoma lines — and six eastbound rush hour trains were canceled, said railroad spokesman Salvatore Arena via email.

“All of the delays on the LIRR tonight are storm related,” the LIRR spokesman said Tuesday. The wind and rain not only cut power to signals and the third rail, but “knocked crossing gates out of commission at multiple locations along both branches,” Arena said.

Commuters frustrated by what they said was disorganization and a lack of communication with riders took to Twitter under the handle #WeDeserveBetter to make their point.

“On the second train, third leg, and 48th minute of my supposedly 27-minute commute,” wrote Great Neck resident Melody Yaghoubi. “Is this the #LIRR or The Oregon Trail?”

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Though the Nassau police said no malfunctioning traffic lights were reported, that was not the case in Suffolk, where West Babylon, Huntington, Hauppauge and Bay Shore reported faulty traffic signals.

Suffolk police put out a statement telling drivers to regard such signals as stop signs because there was concern “that people are not always aware of what they should be doing,” a spokeswoman said.

Almost a dozen nonworking traffic lights were reported, along with trees or large branches blocking several roads, she said.

PSEG Long Island spokeswoman Elizabeth Flagler said, “The crews will work through the night to restore power to everybody.”