The 27-year-old Pinturault won the discipline's season-ending race by 0.68 seconds with seven-time overall champion Marcel Hirscher of Austria, who made a rare appearance in a combined event, coming second.
Slovenia's Stefan Hadalin of Slovenia was third as the rest of the field followed more than a second behind.
Pinturault's main rival, Marco Schwarz of Austria, picked up an injury in the super-G event and was forced to skip the slalom.
"I am really happy but also a little bit disappointed because Marco got injured," Pinturault, who won the silver medal in the combined event at the 2018 Olympic Games, said.
"I wanted to have a great fight. This is bad news. It is a really happy end for me but I think also about Marco," the Frenchman, who became the first male skier to win at least one combined event in seven consecutive World Cup seasons, added.
It was Pinturault's fifth World Cup combined title, equalling the record set by Norway's Kjetil Andre Aamodt in 2002.
(Reporting by Angel Krasimirov; Editing by Christian Radnedge)
