The second seeded Murray had already defeated his German opponent in three sets in the rain-delayed Munich Open final on Monday to register his first claycourt title.
His latest meeting with Kohlschreiber only got underway at just after 1 o'clock after a succession of marathon matches at the joint ATP-WTA tournament had thrown the schedule into chaos.
The Murray-Kohlschreiber clash was not the latest finish to an ATP World Tour tie.
That honour belongs to Benjamin Becker and Jiri Novak who completed a match at the 2006 Japan Open at 03:25.
Murray will have to recover quickly as he is due to face Spain's Marcel Granollers later Thursday for a place in the quarter-finals.
However, Granollers may not be feeling particularly fresh as he needed three hours and 20 minutes to defeat French 13th seed Gael Monfils, 7-6 (8/6), 6-7 (7/9), 6-4.