Jose Irandir Cardoso was arrested after military police who intercepted him at a routine stop on the Brazilian island of Marajo found he was carrying his brother's ID and discovered his true identity after checking his fingerprints at a local station.
Cardoso, one of the Amazon pirates jailed over the 5 December 2001 killing of Kiwi hero Blake, vanished after being sentenced to 32 years in prison.
Local reports said he had been on the run for 16 years.
Last night he was being held at a prison in Breves on Marajo, a large river island bordered by the mouth of the Amazon river in northern Brazil, after being paraded in front of local media by police who captured him.
The violent death of Sir Peter Blake, the world's most famous sailor at the time, had international repercussions
The 53-year-old, knighted in 1995, was monitoring global warming and pollution on the Amazon for the United Nations when his boat called Seamaster was attacked by armed robbers wearing balaclavas and crash helmets.
Blake was fatally shot in the back by one of the assailants after a rifle he had used to defend himself and his crew malfunctioned.
The attackers fled with an outboard motor and some watches after injuring two other crew members with knives.
Ricardo Colares Tavares, the man who shot the Kiwi sailor dead, was later sentenced to 37 years in prison
Jose Irandir Cardoso, found guilty of armed robbery leading to death along with five accomplices from a gang called the Water Rats, was jailed for 32 years.
It was not immediately clear on Thursday how Cardoso went on the run, although it is believed he may have vanished after being allowed to sleep at home under strict house arrest conditions.
Police confirmed only that he had been a fugitive from the Amapa State Penitentiary Service and he had been held around 11pm local time on Tuesday after trying to pass himself off as his brother Sergio Roberto Colares Cardoso.
Sir Peter won the 1989-90 Whitbread Round the World Race and held the Jules Verne Trophy from 1994 to 1997 by setting the fastest time around the world as co-skipper of ENZA New Zealand.
He also led his country to successive victories in the America's Cup, the sport's most prestigious trophy.
He was appointed as a goodwill ambassador of the UN's environment programme five months before his death.
