The unseeded Indo-German pair upset the Poland-Serbian combo 6-4 6-4 in their quarterfinal that lasted one hour and 16 minutes.
With this win, Paes now has a chance to play his first final of the season on ATP Tour. The 43-year-old legend, who has played a number of Challenger level tournaments this season, has seen his ranking plummet to 72.
He won two titles - Biella (Italy) and Busan (Korea) -- on the Challenger circuit.
It was a sort of revenge win for Paes, who had lost to the Polish duo of Kubot and Marcin Matkowski in the Rio Olympics first round along with compatriot Roahn Bopanna.
Paes and Begemann now face third seeds Robert Lindstedt and Aisam-Ul-Haq Qureshi, who got past Marin Draganja and Dominic Inglot 7-6(12) 6-7(4) 10-8 in their close quarterfinal match.
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