The Haradh - Shubaytah test was due to feature 534 kilometres of timed competition in the Rub' Al Khali desert, but worsening weather conditions forced the organisers to end the competitive running early.
Citing "strong wind gusts" and all safety resources being "already mobilised", the Dakar declared the results of the stage at the 223km mark in the car competition.
However, the first half of the planned full stage proved sufficient for Sainz to make up decisive ground relative to his main rivals Nasser Al-Attiyah and Stephane Peterhansel.
Toyota driver Al-Attiyah, who won the Dakar last year and entered Wednesday 24 seconds behind Sainz, started the stage second on the road behind Peterhansel, and was tasked with following the Frenchman "like glue".
Yet both he and Peterhansel got lost trying to find the 223km waypoint, with Al-Attiyah surrendering nearly 15 minutes.
Sainz, meanwhile, came through without major setbacks, ultimately picking up the stage win and inheriting a lead of 18m10s and 18m26s over Al-Attiyah and Peterhansel respectively in the general classification.
Jakub Przygonski (Mini), Giniel de Villiers (Toyota), PH Sport-run Peugeot privateer Pierre Lachaume and Yazeed Al Rajhi (Toyota) made up the top five on the day.
Two-time Formula 1 champion Fernando Alonso, who was 10th heading into the day, rolled his Toyota two kilometres into the stage, which resulted in a long stoppage and forced Alonso and co-driver Marc Coma to remove the windscreen from their Hilux.
He arrived at the 223km waypoint over an hour slower than Sainz, and has dropped down to 14th in the standings.
The competitors will now carefully make their way to the Shubaytah bivouac, where they will not be allowed to receive any assistance from their technical crews under the rally's 'marathon stage' rule.
The last two days of the rally are due to feature around 750 timed kilometres.
General classification (top 10):
Driver / Co-driver
Giniel de Villiers
Bernhard ten Brinke
Jean Michel Polato
Trucks: Shibalov sets the pace
Anton Shibalov ended his Kamaz stablemate Andrey Karginov's streak of stage wins in the shortened test, as he outpaced another Kamaz - that of Dmitry Sotnikov - by one minute in arriving to the 223km waypoint.
Karginov, however, gave up only just over two minutes to Shibalov, and retains a 36-minute advantage heading into the final two days.
Despite the short length, it was a bruising stage for podium contender Siarhei Viazovich, who gave up over half an hour in his Maz but still has a 40-minute buffer over Ales Loprais and an hour in hand over Sotnikov in the fight for third place.
SxS: Lopez setback leaves Currie the clear favourite
Red Bull juniors Mitch Gunthrie and Blade Hildebrand finished the stage 1-2 again in their Overdrive OT3s, while their compatriot Casey Currie took a big step towards his maiden Dakar win.
Though he was six minutes slower than the two Red Bull entries - who are both out of the general classification - at the crucial 223km mark, Currie now has over three quarters of an hour in hand over nearest rival Sergey Karyakin.
Defending champion Francisco Lopez had been a bigger threat coming into the day, but lost nearly an hour to a costly puncture.