Relying on a GPS device placed in a decoy pill bottle, police officers tracked an armed man suspected of robbing a pharmacy on Friday afternoon and fatally shot him during a confrontation on the Upper East Side, police officials said.

The decoy bottle was among a cache of drugs taken in an armed robbery about 1:30 p.m. from HealthSource Pharmacy, at Second Avenue and East 68th Street, according to a police official, who was not authorized to speak about the investigation.

The suspect, identified by the police as Scott Kato, 45, of Mount Vernon, N.Y., was believed to have robbed pharmacies in New York City on at least four occasions since 2011, three times at the HealthSource drugstore. He served about 12 years in prison for a 1990 conviction for sexual abuse and robbery and spent an additional 16 months in prison after violating parole twice, according to state records.

The police official said the GPS device helped lead the police to the man, who was confronted as his 2007 Jeep was stuck in traffic on a service road beneath the Franklin D. Roosevelt Drive at East 96th Street. As officers closed in, the man pointed a handgun in the direction of at least one of the officers; one or more of the officers opened fire, killing the man, the police said.

Police shot the suspect on the Upper East Side of Manhattan. Credit Robert Stolarik for The New York Times The episode is the first known case in New York City in which a decoy bottle helped the police identify a suspect after a pharmacy robbery.

The decoy bottles were introduced last year by the police commissioner at the time, Raymond W. Kelly, who announced that the department would begin to stock pharmacy shelves with decoy bottles of painkillers containing GPS devices. The initiative was in response to a sharp increase of armed and often deadly pharmacy robberies across the state, frequently by people addicted to painkillers.

While the New York Police Department was not the first in the state to use the decoy bottles, it was among the first to publicize the program, believing that the publicity could deter prospective robbers. Other police departments chose to keep the initiatives private, concerned that if robbers knew of the GPS devices, the risk to pharmacy workers could be greater.

The bottles are designed to be weighted and to rattle when shaken, so a thief does not initially realize they do not contain pills. Each of the decoy bottles sits atop a special base, and when the bottle is lifted from the base, it begins to emit a tracking signal.

Nationwide, decoy bottles developed by Purdue Pharma, which makes OxyContin, a brand of oxycodone, have “assisted in the arrest of 111 pharmacy robbery suspects across the country, some of whom have been implicated in multiple pharmacy robberies," said a Purdue spokesman, James W. Heins, adding that the bottle-tracking program had been used in 33 states so far. He would not comment specifically on the case on Friday.

“We have been working with the N.Y.P.D. to implement the bottle-tracking program throughout New York City," he said. “We are reluctant to comment on an active police investigation until the authorities have released additional information."

It was not clear what types of pills had been stolen from HealthSource on Friday, but the police said they believed that Viagra and Cialis, both medications for erectile dysfunction, were taken in one of the other robberies in which they suspected the same man.