Organisers had initially named French Mini driver Guerlain Chicherit as the stage winner.
But that was overturned and Quintero credited with victory after recuperating 95 seconds after stopping for an accident.
The American timed 4hr 35min 08sec on the 413km special around Bisha in Saudi Arabia, finishing 45sec ahead of Chicherit, organisers said.
Defending champion Carlos Sainz (Ford) came in seventh, while five-time winner Nasser al-Attiyah sat in 20th and his Dacia teammate, nine-time world rally champion Sebastien Loeb, in 22nd, 11min 31sec off the lead pace.
"It was a stage without problem for us, we didn't take any risks," said Loeb.
"The goal wasn't to set the fastest time, so we decided to stop for a few minutes at the end to lose some time and avoid starting first tomorrow. Everyone played the same game."
Al-Attiyah added: "The stage wasn't easy, but we took it steady and avoided mistakes.
"In the final kilometres, we had a puncture and stopped for about 15 minutes to make sure we secured a starting position well down the order for tomorrow.
"We gave up a lot of time, but it was important to do so. If I could start 50th, that would be ideal. Last year, we took a risk and learned the hard way."
Competitors will on Sunday tackle a 48-hour stage in the Empty Quarter, a vast sea of sand with dunes as far as the eye can see.
Introduced last year, the stage features a special of 1,000km while drivers and riders have to bivouac on the sand and are not allowed outside help.
Setting off first, or opening the road, is often seen as a disadvantage.
It has been made even tougher this year by the fact that car and motorbike categories will drive differing routes, meaning drivers will be unable to follow the trails set by the faster bikes.
Australia's Daniel Sanders (KTM) took the honours in the motorbike category.
The 30-year-old took the lead at the 151km mark and kept his cool through to the finish, timing 4:41:27 over the special.
Defending champion Ricky Brabec of the US and Botswana's Ross Branch were 2min off Sanders.
