Al Attiyah, the five-time champion, had produced what appeared to be a masterclass in his Dacia as he tried to make up the half-hour he lost the day before and was initially proclaimed the winner of the 428km special stage between Al Ula and Hail.
However, the judges handed him a penalty, which left him just behind Quintero who took his second win of the rally in his Toyota.
"Nasser Al Attiyah received a 10-minute penalty. The explanation is that he arrived with a spare wheel missing from his vehicle," the organisers told the press.
Since the start of the Dakar last Friday, this is the third stage in which the organisers have changed the stage winner after the finish, due to penalties or bonuses.
Quintero completed the stage in 4 hours 32 minutes and 53 seconds, one second better than Al Attiyah's adjusted time. He was a further seven seconds in front of Swedish driver Mattias Ektstrom.
"The first week was pretty good for us, with a victory at the start and two second places. But, on the other hand, we also lost 40 minutes on the '48hr Chrono' stage and with the punctures yesterday," said Quintero, who won stage 1 on Saturday and is ninth in the overall rankings, one and half hours behind leader Henk Lategan (Toyota).
"All in all, it's not too bad. Now, for us it will be upwards and onwards."
South African Lategan, came in fourth. He is 10min 17sec ahead of Saudi driver Yazeed Al Rajhi in the overall standings with Ekstrom third at 20min 54sec.
Defending champion Carlos Sainz withdrew on Monday after rolling his car the previous day while nine-time world rally champion Sebastien Loeb was forced abandon his dream of a first Dakar win after he was ruled out on Tuesday.
Ven Beveren penalised
A time penalty also resulted in a change of winner in the bikes with Argentinian Luciano Benavides on a KTM handed victory after Frenchman Adrien Van Beveren was docked two minutes for speeding on his Honda.
Benavides finished in 4hrs 53min, 47sec ahead of Van Beveren's adjusted time.
"I hope that the strategy will work in my favour for the second week," said Benavides, the 2023 rally-raid world champion.
Chilean rider Jose Ignacio Cornejo Florimo rounded off the day's podium on his Hero.
Australian Daniel Sanders (KTM) remains comfortably in the lead, 7min 2sec ahead of Spaniard Tosha Schareina (Honda).
