The Dutch Iveco driver triumphed by a huge 51-minute 19-second margin over team-mate and countryman Hans Stacey, who was third on the 29km special on the final stage between Pisco and Lima in Peru.
Kazakh Artur Ardavichus of Kamaz was third overall and fifth on the stage.
Italian Miki Biasion, also of Iveco, won the stage in 27:22, 1:26 ahead of Russian Ilgizar Mardeev.
Mardeev, who has endured a disappointing rally, finishes fifth overall behind another Kamaz entry, Andrey Karginov.
De Rooy was thrilled to have won on the 25th anniversary of his father's Dakar victory.
"It's wonderful. I can't believe we already did it this year. It's all thanks to our teamwork. I'm a bit moved, but I'll keep my sunglasses on," he said.
"The entire race was terrific. I was 22 years old when I embarked on this and now, a decade on, we did it exactly 25 years after my father won the Dakar. I was very nervous before the start this morning, but it was a lot of fun. I'm proud of the entire team and my two cabin mates."