Berdych, seeded fourth in Doha, fell 7-6 (9-7), 7-6 (7-4) to the hard-serving Karlovic in a first-round match.
Berdych had an impressive eight aces and faced just one break point, which he saved, but Karlovic fired off 24 aces, saved both of Berdych's break opportunities and survived the tiebreakers.
Karlovic improved to 4-2 lifetime versus Berdych. He beat Berdych in their only other 2013 meeting by taking two tiebreakers in a three-set win.
No. 8-seeded Fernando Verdasco stopped Filippo Volandri 6-3, 6-3 by getting four breaks, including three in the first set.
Tobias Kamke completed Monday's schedule with a 6-3, 6-4 win over Malek Jaziri in just more than an hour. Kamke was able to finish off all three of his break chances and saved five of the six set up by Jaziri.
Also in the first round, Lukasz Kubot came away a 6-4, 6-3 winner over Daniel Gimeno-Traver, while Victor Hanescu had 11 aces in a 6-3, 6-2 decision that eliminated Joao Sousa and Gael Monfils beat Santiago Giraldo 7-6 (7-1), 6-2 as he lost only 11 points in 10 games serving.