The pair - who perform to the music of The Beatles and have been training in Canada - produced an impressive free-skate performance to secure one of the final Olympic spots up for grabs at the Nebelhorn Trophy in Germany.
The top six all secured places at Pyeongchang 2018 in the women's division but, as Germany have already earned one, Weinzierl's place fell to seventh-placed Khnychenkova.
The two-time European bronze medallists scored 105.34 points, setting a new personal best and accumulated 177.13 points overall.
But both the Canadian and the US teams were well out of contention, as Penny Coomes and Nicholas Buckland of Britain won the competition with 177.13 points overall, followed by Kana Muramoto and Chris Reed of Japan with 159.30 points. But since the US already had an Olympic spot secured, the top seven skaters other than Johnson - from Belgium, Sweden (third), Italy (fourth), South Korea, Malaysia (sixth) and Ukraine (seventh) - each took home an Olympic ticket.
Earlier at the Nebelhorn Trophy, Lee June-hyoung locked down a spot for South Korea in the men's singles, but the duo of Kim Su-yeon and Kim Hyung-tae failed to do the same in the pairs.
The run-up to the 2018 Games, however, has gone differently, with North Korea's Olympic chair, Chang Ung, showing support for the South Korean bid, which briefly toyed with the idea using a North Korean ski resort to host part of the competition.
The International Olympic Committee was eager to have North Korean athletes at the Games and has been supporting several of them in terms of equipment, travel and accommodation in their efforts to qualify.
German home favourite Nathalie Weinzierl also took her place on the podium in the Olympic qualifying event, sitting in third in her bid to go to PyeongChang.
The winners of the Nebelhorn Trophy, Evgenia Tarasova and Vladimir Morozov of Russian Federation, had already secured their spot thanks to their performance at the ISU World Figure Skating Championships 2017.
Leading after the short dance, the Britons ensured their advantage was not to be surrendered in Saturday's free dance with a solid performance in Oberstdorf, Germany.
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