Johannes Lochner and Florian Bauer were the first to cross the line after two heats on the German track, ahead of Francesco Friedrich and Thorsten Margis.
The two-time Olympic champion Friedrich, who won the race last week in Altenberg and has been on the podium in eight of this season's nine races, had to settle for second spot after finishing third in the opening heat.
Flock, the 2018 Olympic bronze medalist, had the fastest time in both heats to claim his first World Cup victory since February 2020. Austria's Benjamin Maier, who won the opening race of the season in Innsbruck, was in contention for the podium in third after the first heat but crashed heavily in the second.
The win moved Flock to second in the overall standings, behind Friedrich, with Russian pilot Rostislav Gaitiukevich completing the podium in third.
Flock's Victory
Flock's victory was a welcome return to form for the German pilot, who has struggled for consistency this season but warned last week that he was starting to find his rhythm. His time of 58.87 seconds was just 0.04 seconds faster than Friedrich's in the second heat.
The victory will give Flock a much-needed confidence boost ahead of the World Championships in St. Moritz, Switzerland, in February.
Friedrich's Misstep
Friedrich's second-place finish was a rare off-day for the dominant pilot, who has been in a class of his own this season. The mistakes in the first heat, especially on the lower part of the track, proved costly.
However, with a 39-point lead in the overall standings, Friedrich is still in a strong position to claim a record-extending eighth World Cup title this season.
Maier's Crash
Maier's crash was a big blow to his hopes of challenging for the overall World Cup title this season. The Austrian pilot was on course for a podium finish after the first heat but lost control of his sled in the second and crashed heavily into the barriers.
Fortunately, Maier was not seriously injured but the crash will likely rule him out of next week's race in Sigulda, Latvia.
Flock: "I'm very happy with this victory. I was a bit nervous before the race because this is a difficult track, but I managed to stay focused and make two good runs."
Friedrich: "I made a mistake in the first heat and that cost me the race. I'm not happy with my performance today, but I will learn from my mistakes and come back stronger next week."
Maier: "I'm disappointed with the crash, but I'm also relieved that I'm not seriously injured. I will take some time to recover and then I will focus on preparing for the World Championships."
Flock's victory in Winterberg was a significant result for the German pilot, who has been chasing a return to form all season. Friedrich's second-place finish was a rare slip-up for the dominant pilot, but he remains in a strong position to claim the overall World Cup title.
The crash for Maier was a big blow to his title hopes, but the Austrian pilot will be hoping to recover in time for next week's race in Sigulda.