Nine-time world rally champion Loeb had two punctures on the left side of his Prodrive Hunter and wrestled with a broken hydraulic jack before finishing 16th on the 371km loop around Al'Ula that was won by Toyota's Frenchman Guerlain Chicherit.
Sainz (61), who was 22nd in the stage, had three punctures but was rescued by Audi team mate Mattias Ekstrom providing a spare wheel.
With two stages remaining before Friday's finish in Yanbu, triple Dakar champion Sainz leads Frenchman Loeb by 13 minutes and 22 seconds.
"It was a hard day for us. We had a problem with the (jack) of the car and we had two punctures, so we needed to climb the rocks to find a way to lift the rear tyre to be able to change it," said Loeb, who is chasing a first Dakar win.
"We lost about 15 minutes like this. For sure, it's a bit frustrating, but okay. The stages are hard, it seems Carlos is still losing some time, so at the end, we'll see where we are tonight."
Last year's overall winner Nasser Al-Attiyah, driving a Prodrive Hunter, retired after Tuesday's stage with his hopes of a sixth career win long gone in a spate of mechanical problems.
"Sorry, I don’t want to jump back into this car," he declared before leaving the bivouac. "This year on Dakar, I learned something in my life. It will never happen again."
In the motorcycle category, American Ricky Brabec took the stage win and increased his lead over Botswana's Ross Branch to 10 minutes and 54 seconds, with a second Dakar title looking more and more likely.
"Two days left, the team's looking really strong and I'm 100% right now," he commented.
"Tomorrow, in the big stage... I'm going to use some energy and try and secure something a little bit more so stage 12 is a bit more relaxing for me."
Fellow-Californian Sara Price joined a very short list of female stage winners when she finished fastest in the SSV category.
Price is second overall, 20 minutes behind France's Xavier de Soultrait.
