Crash scuppers Dakar race leader Al-Rajhi's hopes of victory
"The car did a barrel roll and now is damaged," explained Al-Rajhi, who finished third in last year's race.
The 42-year-old Saudi Toyota driver was unable to repair his Hilux after an accident which occurred 51km into the stage, organisers said in statement.
"The crew is safe and sound, but are currently returning to the start of the special," the statement read.
"His hopes of winning the Dakar 2024 have been crushed, but the Saudi driver will be able to start stage 7 the day after the rest day, as long as his 4x4 has been repaired and complies with all the safety rules stipulated by the FIA."
Al-Rajhi was leading Qatari Nasser Al-Attiyah (Prodrive) by 9min 3sec before the start of the stage with Spaniard Carlos Sainz (Audi) third overall at 11min 31sec.
Stage six of the Dakar Rally in Saudi Arabia is an unprecedented two-day event with a 572km special around Shubaytah.
There is a cut-off time of 1500 that will see competitors setting up basic overnight camps and kept in the dark on race positions, before restarting at sunrise on Friday.