Switzerland's Corinne Suter was second, 0.32 slower, in the race in Kvitfjell, Norway, with Germany's Kira Weidle-Winkelmann third.
Overall Crystal Globe contender Emma Aicher finished fourth, 0.01 slower than her teammate, to cut US great Mikaela Shiffrin's overall World Cup lead to 45 points with two races remaining next week - a giant slalom and slalom worth a total of 200 points.
Shiffrin, the most successful World Cup skier of all time, has already won her ninth slalom Crystal Globe and is chasing a sixth women's overall World Cup title.
The American failed to score in the super-G after finishing 22nd, with only the top 15 scoring at World Cup finals. She now has 1,286 points to sole rival Aicher's 1,241.
Goggia had started the day eighth and 63 points clear of New Zealander Alice Robinson, who left the start hut with bib number 11 and already knew her chances of overhauling the Italian had all but gone.
Robinson then narrowly avoided missing a gate and finished 2.41 seconds slower than Goggia, ultimately finishing 16th and 163 points behind.
The Italian, 2018 downhill Olympic champion, has now won five career Crystal Globes -- the others all in downhill.
It was her 29th World Cup win and continued a triumphant weekend for Italy, with Laura Pirovano winning Saturday's downhill to take that Globe while Dominik Paris was the men's race winner.
The men were racing their final super-G later, with Switzerland's Marco Odermatt already having clinched that Crystal Globe as well as the overall one.