The Austrian, Gunther Mader, was third in 2:03.69, while Luxembourg's overall World Cup leader, Marc Girardelli, chasing his first downhill victory for nearly four years, finished sixth.
Victory allowed Heinzer, who also finished third in another downhill in Garmisch on Monday, to pull further ahead in the World Cup downhill standings after five races.
Runggaldier, second behind Heinzer at the 1991 world championship, was delighted with second place after missing last season with a knee injury. It was the Italian's best World Cup placing since he finished second in a downhill in Kitzbuhel two years ago.
In Cortina D'Ampezzo, Italy, Ulrike Maier, of Austria, the world champion, edged the French veteran Carole Merle by 0.2sec to win the women's World Cup super-giant slalom.
It was Maier's third victory of the season - the second in Super-G - , in 1min 16.94sec. Merle, second to the German Katja Seizinger in Friday's downhill, was timed in 1:17.14.
The French skier moved closer to the World Cup overall leader Anita Wachter, of Austria, who finished fifth yesterday.
MEN'S WORLD CUP DOWNHILL (St Anton, Aut): 1 F Heinzer (Swit) 2min 03.48sec; 2 P Runggaldier (It) 2:03.60; 3 G Mader (Aut) 2:03.69; 4 A Skaardal (Nor) 2:03.70; 5 P Ortlieb (Aut) 2:03.79; 6 M Girardelli (Lux) 2:03.89; 7 D Mahrer (Swit) 2:04.03; 8 A Duvillard (Fr) 2:04.13; 9 L Arnesen (Nor) 2:04.41; 10 W Perathoner (It) 2:04.44. GB: 49 M Bell 2:08.23; 53 G Bell 2:08.93. Leading World Cup downhill standings: 1 Heinzer 324pts; 2 Besse 240; 3 Girardelli 209; 4 Stock 188; 5 Mahrer 186. . Leading World Cup overall standings: 1 Girardelli 753pts; 2 A Tomba (It) 472; 3 K-A Aamodt (Nor) 449; 4 Heinzer 436; 5 Mader 344.
WOMEN'S WORLD CUP SUPER-GIANT SLALOM (Cortina D'Ampezzo, It): 1 U Maier (Aut) 1min 16.94sec; 2 C Merle (Fr) 1:17.14; 3 S Eder (Aut) 1:17.25; 4 H Zeller (Swit) 1:17.48; 5= V Zelenskaya (Rus) and A Wachter (Aut) 1:17.50; 7 K Seizinger (Ger) 1:17.62; 8 H Zurbriggen (Swit) 1:17.70; 9 M Ertl (Ger) 1:17.71; 10 R Cavagnoud (Fr) 1:17.87. Leading World Cup super-g standings: 1 Maier 211pts; 2 Seizinger 162; 3 Eder 160; 4 Merle 154; 5 Wachter 137. Leading World Cup overall standings: 1 Wachter 605pts; 2 Merle 583; 3 Seizinger 483.Reuse content