The world number three and top seed in Munich needed just over three hours to seal a 7-6 (7/4), 5-7, 7-6(7/4) win over Kohlschrieber, ranked 24th in the world, who fought hard in front of his home crowd in the Bavarian capital.
It was the 32nd title of Murray's career but his first on clay as he prepares for the French Open at the end of the month.
Heavy rain meant only 23 minutes of the final could be played on Sunday before the match was moved to Monday morning.
It was a gruelling tussle between the pair and was reminiscent of their epic five-setter in their third round at Roland Garros last year when Murray claimed victory after winning the tie-breaker 12-10.
The Scot had little time to celebrate with a bye into the second round at this week's Madrid Masters — where he is set to face Kohlscreiber.
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