David Sweat, 35, is now in custody after being shot by police.
His prison-break partner, Richard Matt, 49, was killed by police on June 26.
The two convicted murderers escaped three weeks ago from the maximum security Clinton Correctional Facility in Dannemora through the sewer system after using power tools to break out of their cell.
The spectacular escape set off a massive manhunt.
David Sweat was shot and seized in the town of Constable on June 28, Franklin County Sheriff Kevin Mulverhill was quoted as saying by the Associated Press news agency.
Sheriff Kevin Mulverhill said the prisoner is now in hospital.
David Sweat was reportedly shot twice. The Buffalo News quoted a source who said that the convict’s wounds were “life-threatening” and he was bleeding badly.
He was spotted by state police and shot when he tried to run away, reports say.
The Bureau of Alcohol, Tobacco, Firearms and Explosives wrote on its Twitter page: “#DavidSweat of the #PrisonBreakNY captured. Sleep peacefully New York.”
Richard Matt was shot dead near the town of Malone.
David Sweat and Richard Matt had been making their way through rugged forests in upstate New York, stealing food and guns from woodland cabins along the way.
US officials have charged prison worker Joyce Mitchell with aiding the two inmates in their escape
Prosecutors allege that Joyce Mitchell gave the men power tools that allowed them to saw through a steel cell wall before bashing a hole through a brick wall and crawling through.
Joyce Mitchell denies the charges.
Clinton correction officer Gene Palmer is also accused of aiding the convicts.
Officials allege that Gene Palmer gave David Sweat and Richard Matt the frozen hamburger meat Joyce Mitchell had used to hide hacksaw blades and a screwdriver.
Gene Palmer’s attorney said his client had no knowledge that the meat contained the escape tools.
Richard Matt was serving a prison sentence of 25 years to life for the killing of his former boss.
David Sweat was serving a life sentence for murdering a sheriff’s deputy.
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