Kieffer finished one shot ahead of the overnight leader, Gavin Green, at the Albatross Golf Resort, near Prague, on Sunday with a 16-under total.
Play had been suspended for the day on Saturday after the course was flooded, following heavy rain shortly after the third round started.
The round resumed on Sunday and the tournament was decided over 54 holes.
The first trophy for the 32-year-old Kieffer came after four runner-up finishes on the Tour.
He also became the first German to win since Marcel Siem captured the 2014 BMW Masters.
Queenslander Jake McLeod finished in a tie for sixth, four shots behind the winner. PHOTO: Ross Kinnaird/Getty Images.
“It’s tough right now to say what it means, I don’t know,” Kieffer said. “It’s great. I’m lost for words.”
Starting the round at four shots behind Green, Kieffer rebounded from a bogey on the 15th with a decisive seventh birdie of the round on the par-4 17th to take the lead.
“I thought I’d need at least another birdie because Gavin was at 17-under,” Kieffer said. “I tried to be aggressive on the 17th.”
Green took a three-stroke lead into the final round but the Malaysian hit the water on the 14th for a double bogey after three birdies, on holes 1, 6 and 10.
This allowed Kieffer and Tapio Pulkkanen of Finland to move level with him at the top of the leaderboard at 15-under.
Green (71) equaled his best Tour result, a runner-up place at the 2017 Hero Indian Open.
Pulkkanen bogeyed the final 18th hole to card 67 and tie South African Louis de Jager (68) for third place another shot back.
Australia’s Jake McLeod shared sixth place after finishing 12-under with a final round of 69.
Zach Murray finished six-under, Maverick Antcliff one-under and Jordan Zunic three-over
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