The 57-year-old led from the third stage and crossed the finish line in Qiddiya 6min 21sec ahead of nearest challenger and reigning champion Nasser al-Attiyah of Qatar, who had managed to cut Sainz's lead to just 24 seconds on Tuesday (Jan 14) but fell back after navigation blunders.
Stephane Peterhansel was third at 9 min 58 sec behind in his Mini. Both the Frenchman and Sainz won four stages each in the marathon 12-day, 7,800-kilometre (4,800-mile) race.
Ricky Brabec won the motorbike section for Honda, becoming the first US rider to triumph in the gruelling race.
This decision to stage the race in Saudi Arabia this year and for at least the next four years sparked an angry reaction from critics of the kingdom's human rights record.