Soukalova, from the Czech Republic, stormed to her second World Cup victory of the season in the 7.5km sprint in Russia on Thursday and she made it three wins in the 10km pursuit 48 hours later.
The 23-year-old battled back from losing the lead at the second shoot to retake it at the fourth and hold on to win by seven seconds ahead of Russian home hope Olga Vilukhina in Khanty-Mansiysk.
Overall World Cup champion Berger placed an important third to pull level with Magdalena Forsberg on 19 podiums for the season with just one more race left to surpass that number in Russia.
Berger, who also won the World Cup title for the pursuit, was out of the picture for much of the race but forced herself into contention at the fourth shoot to take third 14.8seconds behind Soukalova.
The Norwegian now has just the mass start, another discipline where she is the World Cup champion elect, left to better Forsberg's mark that she set on the way to the overall title in 2001.
Soukalova shot clear first time in the range to lead Vilukhina by less than five seconds however the two had swapped places by their next trip with the Russian ahead of the Czech by 6.5seconds.
Both missed one target in the range second time however by the third shoot Vilukhina fell to sixth after two more failures with Vita Semerenko going clear for the third time to take the lead.
Soukalova was clear this time to trail by 6.9seconds however Semerenko missed three targets on her last shoot to drop out of contention with one failure by the Czech giving her the lead.
Vilukhina found her form again to go clear and move into second with Berger now up to third and that was how the top three would stay in the penultimate women's event of the World Cup season.
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