An underground transformer fire sent smoke billowing into Pennsylvania Station yesterday, sickening civilians and causing a power outage that paralyzed Amtrak and Long Island Rail Road service at the station throughout the afternoon, as commuters scrambled for other ways to leave the city.

A transformer in the Amtrak River Tunnel burned up at 12:54 p.m., and it was 7 p.m. before limited rail service “in all three directions” was restored, according to an Amtrak spokesman, Marc Magliari. He said full service was expected to resume by morning.

Mr. Magliari said the outage was sparked when “two wires came together and that caused a sequence of events that resulted in a loss of power.”

The electrical fire occurred 90 feet below the East River in a tunnel that enters Manhattan at 33rd Street and First Avenue and continues on to Penn Station, according to a spokesman for the Fire Department.

The smoke condition was so intense that smoke surfaced at the train station, where five civilians suffered from inhalation. They were treated at St. Vincent’s Hospital.

Power was shut down to safeguard firefighters from electrocution as they doused the flames with dry chemical retardant. A Hazmat squad responded because of toxins related to transformer PCBs, and three firefighters were treated for minor injuries.

Two Manhattan-bound trains from New Jersey, an Amtrak train and a New Jersey Transit train, were temporarily immobilized, as all tracks leading into the station lost catenary power, the overhead source of power that propels the trains, said Mr. Magliari.

The trains did not lose lighting or air conditioning, as those facilities are powered independently. Catenary power was restored within half an hour, and the trains were brought into the station. The rail’s signaling system, however, remained without power for the duration of the outage, resulting in the lengthy shutdown of rail traffic.

From lunchtime through the rush hour, police officers and National Guardsmen turned away rail commuters at Penn Station but informed them that rails were functioning outside the station.

At the main entrance at West 32nd Street and Seventh Avenue, officers with bullhorns directed New Jersey bound commuters down the block to the nearby PATH station.

Commuters bound for Long Island were told to get to the LIRR by subway, taking the E train to Jamaica, Queens, or the 2 or 3 trains to Atlantic Avenue, Brooklyn.

For many Long Islanders, though, the choices were not so clear.

Around 3 p.m., just two hours into the outage, Mike Flanagan of Babylon, stared at the police tape separating the station’s tracks from its bars and newsstands and wondered whether he should seek alternate transport home or simply wait around.

“From experience, I reckon by the time I get to Flatbush Avenue and get on the train, they’ll get the thing fixed, so I’ll just wait here,” Mr. Flanagan, 42, said. “Of course, you might come back four hours later and I might still be here.”

Three hours later, there was no sign of Mr. Flanagan. Another hour, and the rails were running again.

The sentiment of wait-and-see was repeated throughout the outage.

At 6 p.m., Frank Moshfeghi, a jewelry manufacturer from Sayville, stood outside the station, where he had been waiting for 45 minutes.

“Maybe I’ll get a beer, or something,” Mr. Moshfeghi, 47, said. He had just heard from his wife – correctly, he would later learn – that service was soon to resume.

Mr. Moshfeghi wasn’t the only Long Island commuter to see the glass as half-full. Erik Losurdo, an electrician from Bethpage, nursed a drink at Tracks, the Penn Station bar where he had lingered for two-and-a-half hours since getting out of work at 2:30 p.m.

Like many other commuters, Mr. Losurdo, 29, didn’t see the point of packing onto an extra-crowded subway to catch the train farther down the line, when he could enjoy a night on the town instead.

“My girlfriend’s coming to pick me up,” he said. She had just gotten out of work and was driving in from Long Island.

“I figured we just got off work, we’ll make a night of it, go out, have dinner, have a couple drinks, go home,” Mr. Losurdo said.

The manager of Tracks, Liam Whyte, 34, said “the fire downstairs” had severely slowed his rush-hour business. His customers were stranded, but there were fewer around.