Aamodt was only fourth after the first leg of the giant slalom in Adelbolden, Switzerland, and made what he described as a "very big mistake" midway through his second run down the sun-drenched course. But the Norwegian recovered to finish with a combined time of 2min 23.52sec.
"This is incredible," said Aamodt after collecting the 13th win of his career. "After I nearly went down I thought I had no chance to win here. But then Von Gruenigen also made a mistake and that's ski racing. Beating Von Gruenigen on his home turf is an achievement."
Von Gruenigen, the leader after the first run, appeared poised to collect his third straight win and join Alberto Tomba as the only men to sweep the giant slalom classics of Alta Badia, Kranjska Gora and Adelboden in the same season. Victory would have also virtually secured this year's giant slalom World Cup for Von Gruenigen who also won it last year.
On the second run Von Gruenigen was urged on by thousands of Swiss supporters lining the course but he finished 0.17sec slower than Aamodt, with an aggregate time of 2:23.69.
"Nobody is unbeatable but it's tough to lose on your home ground," said Von Gruenigen, who has now reached the podium in all but two of the last 15 giant slaloms.
"My second run just was not good enough. I made mistakes, but all has gone well this winter. I was second today and that's not so tragic. Maybe I was trying too hard. But I won this race last year and I'm pleased with a place on the podium. You have to be ready for victory and for defeat."
Austria's Andreas Schifferer, 13th after the first leg, recorded the fastest second run to leap into third place with 2:23.96.
Hans Knaus, second behind Von Gruenigen after the first leg, fell at the bottom of the piste and missed the final gate. Knaus was one of several Austrians to run into trouble in the race as the nation's skiers competed fiercely for places in the team for next month's World Championships.
Von Gruenigen's second place left him in a strong position at the top of the giant slalom standings and also in the lead in the overall World Cup, ahead of Aamodt. With two giant slaloms remaining and 200 points on offer, Von Gruenigen leads Aamodt by 159 points in the discipline.
The win put Aamodt, the 1994 overall champion, back into the fight for a second title. The Norwegian all-rounder now trails Von Gruenigen by just 26 points in the overall standings. "I'm thinking about the overall title," admitted Aamodt, who also has three third-place finishes to his credit this season. "But I'm taking things one race at a time and hope I can get on a roll."
The Norwegians had further reason to celebrate as Lasse Kjus, the reigning overall World Cup champion, returned to competition. Bothered by chronic sinus problems, Kjus has been out of action since the circuit returned to Europe from North America in December.
"I've only been training four days so I was really worried about my fitness," said Kjus, who finished seventh. "So under the circumstances I'm very pleased with my performance."
There was no such good news for Tomba, who missed the race because of the influenza that forced him out of the second leg of the slalom in Chamonix on Sunday. Tomba's absence could prove costly in his bid to defend his giant slalom title at the World Championships as he dropped out of the top 15 in the giant rankings for the first time in 10 years.
That means Tomba will not be able to select a start number at the World Championships in Sestriere, Italy.