Orlando JosÃ© Figuera suffered burns to 80% of his body after he was engulfed in flames. Officials said he was also stabbed in Saturday's protests.
Witnesses said the crowd had accused the man of being a thief.
On the same day, an opposition activist was shot dead, bringing the total number killed in recent protests to 48.
The attorney general's office said gunmen allegedly opened fire on the demonstrators in the western city of Valera.
Edy Alejandro Teran Aguilar died from a gunshot wound to the chest, while two others were wounded.
Protesters demanding President Maduro step down and hold elections took to the streets across the country on Saturday to mark the 50th day of the increasingly violent demonstrations which have overwhelmed the country in recent weeks.
"A person was set on fire, beaten up, stabbed... They nearly lynched him, just because he shouted out that he was a 'Chavista'," President Maduro said, referring to the ruling Socialist movement set up by his predecessor Hugo Chavez.
Speaking on his weekly TV programme, Mr Maduro described it as  "a hate crime and a crime against humanity".
It is thought 46 people were injured in the demonstration in eastern Caracas where Mr Figuera, 21, was hurt.
Journalist and politician Earle Herrera said the man had been accused of being a thief, according to Globo.com [in Spanish].
Venezuelan Information Minister Ernesto Villegas tweeted it was "growing insanity".
"A human being is set on fire at a 'peaceful demonstration' by the opposition in Caracas," he wrote, posting a video of the incident.
Protests have been taking place across Venezuela for seven weeks, as anger towards Mr Maduro and his government rises.
Seven in 10 people are said to oppose Mr Maduro, according to private surveys.
Despite having the world's largest known oil reserves, Venezuela is facing a shortage of many basic items, including food and medicines.
Its economy has collapsed, with inflation expected to top 700% this year, and crime is rampant.
The opposition is calling for early elections and the release of opposition politicians jailed in recent years, saying the socialist governments of Mr Maduro and his predecessor, the late Hugo Chavez, have mismanaged the economy since coming to power in 1999.
Venezuelan President Nicolas Maduro has accused opposition protesters of setting alight a government supporter in Caracas on the 50th day of protests.