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Samsonova became the first qualifier to reach a WTA 500 final this season by shaking off Victoria Azarenka in the semis and followed that up with victory over fifth seed Bencic.
The world number 106, competing in her first career final, held serve in the final two sets to win 1-6 6-1 6-3 in a time of one hour and 37 minutes in Berlin.
Bencic was seeking a fifth WTA title and stormed into a 5-0 lead in a one-sided opening set, but Samsonova soon found her rhythm and hit back in the second.
The Russian broke her opponent's service game in the second and fourth games to level up the contest and earned an early break in the deciding set.
Samsonova did not look back and got over the line on her second championship point by forcing Bencic into a netted backhand with a strong return.
She ended the match with 28 winners to just 15 unforced errors and will move into the world's top 100 following victories over Madison Keys, Azarenka and Bencic in this breakthrough week.