Eleven people died -- some reportedly electrocuted while looting a bakery, and others shot -- and six people were wounded in riots in the capital's southwestern district El Valle, the public ministry said in a statement.
The neighborhood witnessed pillaging and violent clashes between police and protesters, according to residents, some of whom took images of an anti-riot vehicle charred by Molotov cocktails.
"It was like a war," resident Carlos Yanez told AFP.
The opposition accuses the government of sending gangs of armed thugs to attack them, and says the security forces have been repressing protesters.
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Videos taken by locals showed residents throwing bottles and other objects out their windows at the gunmen in the streets below, shouting "Murderers!"
At one point, street protesters throwing Molotov cocktails managed to set fire to one of the armored police trucks firing tear gas at them, lighting up the night sky.
There were conflicting explanations why.
The government said "armed gangs hired by the opposition" had attacked the hospital. The opposition rejected the allegation, saying the children had to be evacuated because of tear gas fired by Maduro's "dictatorship."
Riot police firing tear gas also fought running battles with protesters overnight in eastern Caracas.
Besides the 11 people killed in El Valle, another man was shot dead in the Petare neighborhood in the east, said the local mayor.
"We demand that the culprits be investigated and punished," said Mayor Carlos Ocariz, a Maduro opponent. Prosecutors said they had opened an investigation.
The two sides looked set to spend the day regrouping after massive protests Wednesday and Thursday erupted into unrest in the flashpoint western city of San Cristobal and several other cities.
Opposition leaders have called new protests for Saturday and Monday.
On Saturday, they plan to march in silence to the Catholic Church's episcopal seats nationwide. They plan to erect roadblocks on Monday to grind the country to a halt.
Maduro says the protests seeking to oust him are part of a US-backed coup plot.
On Thursday, he said the opposition had agreed to new talks, but his opponents denied the claim, saying the only way forward was to call elections.
Senior opposition leader Henrique Capriles slammed Maduro as a "dictator" and "mythomaniac."
Pressure on Maduro has been mounting since 2014, as falling prices for Venezuela's crucial oil exports have sent the once-booming economy into a tailspin.
The court partly backtracked after an international outcry, but tension only increased when the authorities slapped a political ban on Capriles on April 7.
Hundreds of thousands took part in Wednesday's marches, in which a 17-year-old teenager and a 23-year-old woman died after being shot in the head by masked gunmen. Maduro's camp said a soldier was also killed.
The ruling Socialist party accused the opposition of sowing violence to chase headlines.
Figures published by pollster Venebarometro show seven in 10 Venezuelans disapprove of Maduro, whose term does not end until 2019.