Overall World Cup leader Aksel Lund Svindal of Norway and Max Franz of Austria shared third, 0.15 off the lead.
The top 34 finished within a second of the winner, but defending overall champion Marcel Hirscher of Austria finished 1.58 off the lead and lost further ground to Svindal, who now leads the Austrian 897 to 735 points.
"I knew the times would be very close," Defago said. "From the first gate I felt my equipment was really great today."
The super-G results also count as the first leg of a combined event, with a slalom run to follow later Sunday. Speed specialist Defago will skip the slalom, leaving Miller as the leader in that competition.
Organizers delayed the super-G for three hours due to snowfall and lowered the start because of strong winds.
Defago won the Olympic downhill title in 2010 but missed the following season after tearing ligaments in his left knee. He hadn't been on a World Cup podium since his win in Bormio.
However, getting top-10s in three downhills this season, including last week in Wengen and Saturday in Kitzbuehel, were signs of a return to form with the Sochi Olympics looming.
"It's yet unclear if I am really going to retire," said the 36-year-old Defago, who had earlier hinted this Olympic season might be his last. "When I see I can still race this good then it becomes a difficult decision."
Miller missed out on a possible win for a second straight day after mistakes he called "heartbreaking" and "painful" saw him come third in the downhill. He had targeted that race to earn his first World Cup win since taking the downhill in Beaver Creek in 2011.
Miller said the anger from the day before helped him in the super-G. Starting 23rd, he was clean throughout and beat the times from the season's leading super-G racers.
"You use the emotions if you can, if you think that's beneficial," Miller said. "I know that on a short course, skiing really aggressive, really angry, can be helpful because it's so really close. When it comes down to five-hundreds ... a little bit of extra aggression can make the difference. I definitely brought that in there and that's just a usable emotion."
Miller added that he "skied really well. I didn't leave a whole lot out there. Second place is also fine. Both results are fine, I am just much happier with my skiing today."
Miller considered himself unlucky having to start right after a scheduled TV commercial interruption of the race.
"It doesn't help to have the TV break right before you," Miller said. "Three minutes of nobody skiing the actual track. And the snow, it's not very much but it's enough to slow things down a little bit."
World super-G champion Ted Ligety was 0.94 back in 31st, but American teammate Travis Ganong trailed by 0.30 in sixth for his career-best result in the discipline.
"My skiing is in a really good spot right now," said Ganong, a day after finishing seventh in the downhill. "You get to the point where you've done so many races, you turn your brain off and you just ski and have fun. Most races I've done in the past, I've been over-thinking things. This run I just forgot about everything just relaxed and skied and had fun."
Ganong inspected the course on his powder skis and went powder skiing as his warm-up for the race.
"That was a good move," Ganong said. "There are a couple of really tough turns that you have to nail but other than that you just shut your mind off and go, go, go."
The weekend's World Cup races are the last before nations have to name their squads for the Sochi Olympics.
Men's World Cup Super-G Results
At Kitzbuehel, Austria
1. Didier Defago, Switzerland, 1:10.38.
2. Bode Miller, United States, 1:10.43.
3. Aksel Lund Svindal, Norway, 1:10.53.
3. Max Franz, Austria, 1:10.53.
5. Johan Clarey, France, 1:10.57.
6. Travis Ganong, United States, 1:10.68.
6. Otmar Striedinger, Austria, 1:10.68.
8. Carlo Janka, Switzerland, 1:10.73.
9. Adrien Theaux, France, 1:10.74.
10. Markus Duerager, Austria, 1:10.79.
11. Kjetil Jansrud, Norway, 1:10.80.
12. Georg Streitberger, Austria, 1:10.92.
13. Matthias Mayer, Austria, 1:10.98.
13. Romed Baumann, Austria, 1:10.98.
15. Vincent Kriechmayr, Austria, 1:10.99.
16. Joachim Puchner, Austria, 1:11.01.
17. Patrick Kueng, Switzerland, 1:11.04.
18. Alexis Pinturault, France, 1:11.07.
19. Thomas Mermillod Blondin, France, 1:11.11.
20. Peter Fill, Italy, 1:11.12.
21. Morgan Pridy, Canada, 1:11.17.
22. Steven Nyman, United States, 1:11.18.
23. Andrew Weibrecht, United States, 1:11.22.
24. Brice Roger, France, 1:11.25.
25. Stephan Keppler, Germany, 1:11.26.
25. Rok Perko, Slovenia, 1:11.26.
25. Christof Innerhofer, Italy, 1:11.26.
28. David Poisson, France, 1:11.27.
29. Jan Hudec, Canada, 1:11.29.
30. Klaus Kroell, Austria, 1:11.31.
31. Ted Ligety, United States, 1:11.32.
32. Jared Goldberg, United States, 1:11.33.
44. Marco Sullivan, United States, 1:11.57.
50. Tim Jitloff, United States, 1:11.76.
54. Erik Fisher, United States, 1:11.83.
71. Mark Engel, United States, 1:12.92.
77. Bryce Bennett, United States, 1:13.29.
World Cup Super-G Standings
(After four of six races)
1. Aksel Svindal, Norway, 296 points.
2. Didier Defago, Switzerland, 162.
3. Patrick Kueng, Switzerland, 159.
4. Bode Miller, United States, 138.
5. Georg Streitberger, Austria, 134.
5. Otmar Striedinger, Austria, 134.
7. Jan Hudec, Canada, 128.
8. Kjetil Jansrud, Norway, 127.
9. Matthias Mayer, Austria, 126.
10. Max Franz, Austria, 117.
19. Travis Ganong, United States, 64.
23. Ted Ligety, United States, 45.
27. Andrew Weibrecht, United States, 29.
39. Steven Nyman, United States, 9.
47. Erik Fisher, United States, 3.
Overall World Cup Standings
(After 22 events)
1. Aksel Lund Svindal, Norway, 897.
2. Marcel Hirscher, Austria, 735.
3. Alexis Pinturault, France, 569.
4. Felix Neureuther, Germany, 491.
5. Hannes Reichelt, Austria, 476.
6. Ted Ligety, United States, 449.
7. Bode Miller, United States, 449.
8. Patrick Kueng, Switzerland, 398.
9. Henrik Kristoffersen, Norway, 341.
10. Adrien Theaux, France, 336.
33. Travis Ganong, United States, 164.
53. David Chodounsky, United States, 84.
62. Tim Jitloff, United States, 63.
69. Marco Sullivan, United States, 54.
82. Steven Nyman, United States, 35.
83. Jared Goldberg, United States, 33.
84. Andrew Weibrecht, United States, 32.
87. Erik Fisher, United States, 30.
112. Nolan Kasper, United States, 13.
129. Robbie Kelley, United States, 3.