Sainz was 25th at the end of the stage, 59 minutes in arrears of rally leader Yazeed Al-Rajhi in his Toyota HiLux.
Overall, Sainz is 22nd, sitting 49 minutes and 33 seconds off the race-leading pace.
Sainz was only three minutes and 27 seconds off the lead before the crash.
Teammate Mitch Guthrie Jr. assisted Sainz, helping flip the car back onto its wheels.
“Today has been quite a complicated stage,” said Sainz, who had been eighth at the end of Stage 1.
“After rolling over on a cut dune, we were able to continue thanks to the help of our team-mate Mitchell, but then we had more problems.
“The car was overheating, we couldn’t see well because of the broken glass and we punctured. The day went from bad to worse.”
Sainz was a little more than 325km into the marathon 48-hour stage when he crashed.
The Ford Raptor suffered damage, mostly to the rear bodywork.
Despite the crash, M-Sport Ford team principal Malcolm Wilson offered some optimism.
“Carlos, unfortunately, had a problem at around kilometre 327,” Wilson explained.
“At that point, he was in first or second place, we’re not sure, so he was opening up the track.
‘He was on a dune and they landed upside down, with the roof of the car on the ground.
“Mitch managed to help him, and then he stopped for a while to obviously move some damaged parts and that sort of thing.
“It looks like, from what we’ve seen, there’s no structural damage. It’s been running at a reasonable pace, flat out after the accident.
“[All the Fords] will be together and hopefully we’ll have a chance to implement repairs.
“Then, the most important thing is to bring him back tomorrow, and from what seems to have been lost, it’s maybe around an hour, which on the second stage of the Dakar is a lot.
“There’s a long way to go.”
Ford’s leading Raptor is driven by Mattias Ekstrom, who sits fourth overall.
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