Neureuther, who limped off the course after crashing out in Saturday's giant slalom, said he had three early morning injections to fight his injury.
"After the way I felt, to stand here as the winner, it's a little miracle that I could do it," said the 28-year-old German, who hung on to his opening-leg lead. "I couldn't believe how fast I was."
Neureuther won his second slalom of the season by finishing 0.36 seconds ahead of Austrian Hirscher in a two-run time of 1 minute, 52.20 seconds. The German finished second in the standings.
Hirscher already won the season-long slalom title and ensured he finished on the podium in all nine World Cup races in the discipline.
"I'm happy with the whole season," said the 24-year-old Hirscher, who matched Alberto Tomba's record of top-3 finishes in a nine-race slalom program. The Italian great achieved it in the 1991-92 World Cup season.
"It's unbelievable for me to be in the same rank," Hirscher said.
Hirscher's dominating season in slalom included the world championships gold medal last month in Schladming, Austria.
Ivica Kostelic, the 2011 overall World Cup champion from Croatia, was third Sunday, trailing Neureuther by 0.51.
The podium placings were the same when Neureuther won in January at Wengen, Switzerland.
In 20 World Cup events, Hirscher had 18 top-3 finishes, and he was set to win the GS at Adelboden, Switzerland, when maling a big error near the end. His other miss was a rare start in super-G at Beaver Creek, Colorado, where he placed 32nd.
Hirscher added 80 World Cup points Sunday to complete his season with 1,535 overall. He had 180 more when he won the giant crystal globe trophy for the first time last season.
Aksel Lund Svindal of Norway, who skips slalom races, finished second with 1,226. Ted Ligety of the United States placed third with a career-best total of 1,022.
The giant slalom specialist skied out midway through the first slalom run, one day after winning his sixth World Cup race this season.
"It's the story of my slalom season," said Ligety, who has targeted improved results in the most technical discipline to challenge Hirscher next year.
American teammate David Chodounsky also skied out as only 18 of 26 starters completed the first leg on a tricky snow surface.