The incidents came ahead of Sunday's presidential election in which Socialist incumbent Nicolas Maduro, who has been accused of using the detention facility to crack down on opponents, is seeking a second six-year term in the crisis-hit nation whose economy is crippled.
"We want to inform the country that as of now the installations are under the control" of the authorities, opposition figure Villca Fernandez said in an audio message sent by internet from his cell in the Sebin intelligence service's Helicoide center in Caracas.
Dozens of opposition prisoners launched the protest late on Wednesday, demanding the immediate release of 20 inmates who have been ordered free on bail, speedier court processes and medical care.
Fernandez said that following negotiations with the prosecutor's office, dozens of inmates are to be transferred from Sebin to other facilities.
"We achieved freedom for the four minors... and the transfer elsewhere of 68 common prisoners to their respective detention centers," he said.
Venezuela's state prosecutor Tarek William Saab on Thursday said 72 prisoners were being transfered following talks with the protesters.
A total of 256 prisoners are being held at the facility, including 54 for "political reasons", according to the prisoners' rights group Foro Penal.
The United States on Thursday expressed "serious concerns" over the standoff with Venezuelan authorities after an American man among the prisoners, Joshua Holt, pleaded for help in a video sent via Twitter.
"I'm calling on the people of America. I need your help to get me out of this place," said Holt, who was detained in 2016.
Holt was arrested by Sebin and accused of possessing weapons and plotting to destabilize the Maduro regime. Top officials in the Socialist government have labelled him a US spy.
On his Twitter account, Daniel Ceballos, a former opposition mayor of the city of San Cristobal, published a photo of a group of prisoners, including Holt, gathered inside the center.
Saab said the protest began after one prisoner beat Gregory Sanabria, one of the imprisoned opposition figures, who then took over a "small corridor" at the entrance of the prison.
It remains unclear how the inmates took control of the space as they were not armed, nor how they could send videos and photos of what happened.
"We got out of a situation that could have been very dangerous," Saab told state television, indicating he believed the takeover was intended to tarnish Sunday's election.
In audio and video messages, the opposition prisoners appealed for a boycott of the vote in line with a call by the coalition of opposition parties, which has labeled the election as a "farce" to maintain Maduro in office.
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