The 28-year-old native of Graubünden, who had only one World Cup win and podium so far, won with a combined time of two minutes 45.20 seconds, after one downhill and one slalom run.
The win came after Swiss cross country skier Dario Cologna, also from Graubünden, clinched his second gold medial at the Sochi Games in the 15-kilometre Nordic skiing classic.
Croatian veteran Ivica Kostelic was second in the super-combined, 0.34 seconds behind, bagging his fourth Olympic silver and third in the combined.
He preceded Italy's Christof Innerhofer 0.47 seconds adrift, who takes his second medal at these Winter Games after downhill silver on Sunday.
The result turned all predictions upside down as combined world champion Ligety and young gun Pinturault failed to even make the top ten in the Valentine's Day race.
The two skiers had each won one super-combined race this World Cup season.
But Ligety, who needed a clean slalom after finishing 18th in the morning's downhill, made a costly mistake and ended up 12th.
France had meanwhile set its sights on Pinturault to win a first alpine skiing medal for the country in Sochi.
But the 22-year-old, who won the super-combined in Kitzbühel last month, straddled a gate even as he was leading in the times, and went out.
Defending Olympic champion Bode Miller, seeking to make up for a disappointing eighth place in the downhill, fought hard to come back from a 12th place after the morning run but had to make do with sixth place.
The tricky course, made even more challenging by warm temperatures, left several casualties in its wake, including Italy's Peter Fill, US skier Andrew Weibrecht, Austrian Max Franz and Norway's Aleksander Aamodt Kilde.
With lumpy snow and a tough course set by Ante Kostelic, Ivica's father, many straddled or caught their skis in a gate and fell.