Junghaenel took the gold medal with a final score of 210 points, 2.1 points ahead of his rival here on Thursday.
"It definitely was a good day for me," Junghaenel said after winning.
"I started off a little bit on the right but once I fixed that the final was pretty awesome."
"After I placed sixth in Bangkok, I made some adjustments, but I didn't expect a win here. I'm pretty happy about it. It's been a great final. No doubt about that. The range needs some minor fixes but you can already say it's a good range."
Serbia's Steven Pletikosic won his first medal in this event since 2008, taking bronze with 186.2 points.
The World Cup series stage in Rio is also serving as an official test event for the Olympic Games in August. (IANS)