Dramatic footage posted by Perez on social media showed him with a bloody face saying he was surrounded by police shooting at him with grenade launchers.
State television later revealed two police officers have been gunned down during the clash, but did not say what happened to Mr Perez.
President Nicolas Maduro’s leftist described him as a “fanatic, extremist terrorist”.
A manhunt had been underway for months after Oscar Perez used a stolen helicopter to drop grenades on the Supreme Court in June last year during anti-government protests.
Authorities tracked him down in a poor hillside village called El Junquito on Monday.
Posting a video on Instagram, a visibly injured Perez told his children he loved them and hopes to see them again.
Wearing a bulletproof vest, he looked into the camera and said: “We’re wounded … they’re killing us!
“Venezuela, don’t lose hope… Now only you have power so that we can all be free.”
Gunshots can be heard in the background. He posted his last video at 2.30am GMT.
Mr Perez, who has been an action film star, styles himself as a James Bond character on social media and has add further drama to Venezuela’s tumultuous political sphere.
He gained notoriety in June after allegedly hijacking a police helicopter, flying over Caracas’ centre and firing shots at and lobbing grenades on the Interior Ministry and the Supreme Court.
Perez claimed responsibility for the attack, saying it was to fight what he said was a tyrannical government.
In December, a video posted on Perez’s YouTube account shows armed, masked men taking control of military barracks under cover of night.
They smashed photos of Maduro and his predecessor, the late Hugo Chavez, handcuffed about a dozen soldiers and berated them for supporting “dictatorship” in Venezuela.
Perez says his team stole about 26 AK-103’s and more than 3,000 munitions for the rifles, as well as pistols.