Walther and brakeman Christian Poser crossed the line with a combined time of one minute 38.39 seconds -- a lead of 0.10 seconds over Kripps.
The German pair took the final curve so quickly that their sled overturned and Walther and Poser hurtled across the finish line with their helmets scraping along the wall of the ice track at the Olympic Sliding Centre.
Neither athlete was injured.
In the first heat, Latvia's Oskars Melbardis led the field but the Sochi gold medallist was unable to maintain that pace in heat two, slipping to fourth place.
That paved the way for Walther's team mates Johannes Lochner and world champion Francesco Friedrich to creep up the timesheet to third and fifth places, putting the German team in an overall strong position ahead of Monday's final.
Germans have long dominated the two-man bobsleigh event at the winter Games -- bagging seven golds since 1928.
Canada's Justin Kripps had the most consistent runs, however, placing second in both heats.
Kripps, who tops the International Bobsleigh & Skeleton Federation (IBSF) pilot rankings, is hoping to match his World Cup success at the Games.
A gold from Kripps would be Canada's second in the two-man competition since Pierre Lueders's victory in Nagano in 1998, and the 31-year-old heads into the final heats in a good position to get it.
"I want a medal but I don't need one," Kripps told reporters after Friday's training. "If we don't, I'll be disappointed but at the same time, give me five minutes and I'll be smiling again."
An ice temperature of minus 11 degrees Celsius made for a glisteningly-fast track for Sunday's race.
Loaded with their pilots and brakemen, the 360-kg sleds blistered past spectators with a roar like a fighter jet at speeds of more than 130kph.
Although some seats have remained empty at the Games in Pyeongchang, the Olympic Sliding Centre has been abuzz with spectators thanks to South Korean Yun Sung-bin's skeleton victory on Friday.
"Wow! So many people on the track to watch the first two heats of the two-man bobsleigh competition!" the IBSF tweeted on its official account.
(Editing by Clare Fallon)
