De Mevius finished the 414km stage from Al'Ula to Al Henakiyah one minute and 44 seconds clear of Audi's second-placed Spaniard Carlos Sainz.
Toyota's South African Giniel de Villiers was third overall but nine minutes and 18 seconds off the pace.
"I'm quite surprised, to be honest; we drove smart and avoided punctures and I think that was the key today. But I'm quite surprised to finish so high up," said de Mevius.
The day's big losers were Al-Attiyah, the reigning champion, and nine-time world rally champion Loeb - both driving Prodrive Hunters.
Frenchman Loeb was 18th and more than 22 minutes adrift while Al-Attiyah, a five-time Dakar champion and winner for the past two years, was 21st.
"In the first 50km, we had two punctures and then we cannot push. We just tried to manage (to reach) the finish," said Al-Attiyah.
Dakar record holder Stephane Peterhansel, a 14-times winner on two wheels and four, was 23rd.
The start of the first car was delayed after an incident with a spectator, who was taken to hospital, some 200 metres into the stage.
There was an immediate shock in the motorcycle category when Honda's prologue winner Tosha Schareina retired with a broken left wrist after 240km.
"I tried to pass (Australian) Toby (Price) and I think I hit something with the rear wheel. I crashed in slow (speed) but I broke my wrist," he said.
Botswana's Ross Branch, who stopped to help Schareina and was credited with the lost time, led the motorcycle category after winning the stage ahead of Americans Ricky Brabec and Mason Klein.
In the SSV category, Brazilian Rodrigo Varela led after starting in a borrowed car after the ship carrying his original vehicle had to divert its route to escape Houthi pirates in the Red Sea and was delayed.
Sunday's stage is 463km from Al Henakiyah to Al Duwadimi.
