The fatal accident occurred after 276 kilometers in Sunday's stage between Riyadh and Wadi ad-Dawasir.
He was unconscious when medical personnel arrived at the scene and was flown by helicopter to hospital, where it was found that he was dead.
Goncalves drove the Dakarrallyt for the 13th time and was in tenth place in the motorcycle class summary. His best result in the competition came in 2015, when he won one stage and finished second overall.
Goncalves turned 40 years old.