Jose Sanchez and Alejandro Sanchez were arrested "for organizing terrorist acts and assaults against the peace of the country," Interior Minister Nestor Reverol wrote on Twitter.
The two are youth leaders of the Justice First party, one of the main groups in the center-right opposition coalition pushing for President Nicolas Maduro to be removed from office.
Venezuelan authorities drew international criticism last week for banning the party's most prominent figure, Henrique Capriles, from public office for 15 years.
Reverol said the two detainees "confessed taking part in this week's violence."
Five people, including a 13-year-old boy have been killed since April 6 in clashes with riot police during a wave of protests against Maduro.
Justice First rejected Reverol's allegations. It wrote on its Twitter account that the two youth leaders were "abducted" by military intelligence forces.
"Nestor Reverol, the real terrorism is the one you are leading by repressing the people," it wrote.
Police fired tear gas and rubber bullets to disperse protesters in Caracas in the latest eruption of unrest on Thursday, AFP reporters saw.
Maduro is fighting off efforts to oust him as Venezuela, once a booming oil-exporting nation, struggles with shortages of food and medicine.
The next major organized rallies called by opposition leaders are set for Wednesday next week.
That is expected to be the next big showdown in an increasingly fraught crisis that has raised international concerns for Venezuela's stability.
The opposition is demanding the authorities set a date for postponed regional elections.
It is also furious over moves to limit the powers of the legislature and ban Capriles from politics.
Those moves have raised international condemnation including from the United States and the European Union.
Maduro has resisted opposition efforts to hold a vote on removing him, vowing to continue the "socialist revolution" launched by his late predecessor Hugo Chavez.
Maduro says the economic crisis is the result of what he calls a US-backed capitalist conspiracy.
Eyewitness? Submit your stories now via social or:
Email: news@pulselive.co.ke
