But mystery surrounds how the 39-year-old Pole lost his life.
No damage was found to either his body or bike, said race director Etienne Lavigne.
Hernik, who was located just a few hundred meters from the race track, had removed his helmet prior to his death.
"The circumstances surrounding his death have yet to be determined, as the competitor did not show any external signs of an accident," said a rally statement.
Hernik -- who was competing in his first Dakar -- was found at kilometer 206 on the stage between San Juan and Chilecito, in northern Argentina.
Shortly after the rider, wearing bib number 82, failed to appear at the finish line, organizers tried to find him.
The search was complicated by the absence of a signal from his satellite tracker.
"When the race management detected the loss of his Irritrack signal and was informed that he had not completed the special stage at 15:16, it decided to start a search for the rider at 15:23," said a statement.
"An ambulance helicopter found the rider 300 meters off the route at 16:03.
"Unfortunately, the on-board doctor could only confirm the rider's death."
Hernik's death means five competitors have died since the rally moved from West Africa to South America in 2009 because of security concerns in the Sahara region.
All those five have been competing in the motorbike section.
Since the Dakar began on December 26, 1978, a total of 24 competitors have died but there have been over 50 fatalities when including the deaths of spectators and officials.
Speaking after the stage, the overall leader of the motorbike race -- Joan Barreda Bort -- said it had been a challenging section.
"It was really dangerous because we were on river beds with a lot of stones and broken up tracks all day," the Spaniard told reporters.
Race organizers said Hernik had previously competed -- and completed -- both the 2013 Morocco Rally and the 2014 Abu Dhabi Desert Challenge.
"The whole Dakar family offers its condolences to Michal's family, close friends and team," added the Dakar statement.