The pair's performance in the streets of the Azerbaijani capital also earned them the FIA GT title.
"When the team told me over the radio that I was leading the race, I was thinking that they were making a joke," admitted 22-year-old Vanthoor.
"My aim was (just) to bring the car home in one piece, as it was easy to make mistakes," the Belgian, who had not won a major title since topping the German F3 championship in 2009, added.
|Podium in Baku (Photo: FIAGTSeries.com)|
"It feels so fantastic!"
Vanthoor and Ortelli's WRT teammates René Rast and Niki Mayr-Melnhof helped secure the teams' championship with a win of their own in qualifying.
Alvaro Parente and Sébastien Loeb, of Loeb Racing, finished fourth.
McLaren protege Stoffel Vandoorne failed to reach the finish, sharing a McLaren MP4-12C with countryman Frédéric Vervisch.