The 75-year-old, who had lived under police protection since 2007, after being subjected to death threats over the cartoon, was travelling in a civilian police vehicle which collided with a truck near the town of Markaryd in southern Sweden.
Two police officers were also killed and the truck driver was injured.
Vilks’ 2007 cartoon offended many Muslims who regard visual representation of the Prophet as blasphemous.
The cartoon led then Prime Minister Fredrik Reinfeldt to meet ambassadors from 22 Muslim countries in an attempt to defuse the situation.
Speaking to a journalist in Stockholm at the time, Vilks said: “I’m actually not interested in offending the prophet. The point is actually to show that you can.
“There is nothing so holy you can’t offend it.”
Shortly after the publication of the cartoon, al-Qaeda offered a £73,692 reward for his murder – with an extra $50,000 if a knife was used.
In 2015, Vilks attended a debate on free speech that was targeted in a gun attack in Copenhagen, which killed a film director.
The attack came just over a month after gunmen stormed the Charlie Hebdo offices in Paris, killing 12 people.
Police have not revealed the identity of those killed in Sunday's incident, but Vilks' partner confirmed his death to Dagens Nyheter newspaper.
In a statement, police said it was the circumstances leading to the collision was still unclear – but there was nothing to suggest that anyone else was involved.