The 21-year-old Tomic, whose rollercoaster career took another twist when he split with global management company IMG last week, defied the 39 aces of Karlovic to take victory in two hours and 13 minutes.
It was his second tour-level title, adding to a 2013 triumph at the Sydney International.
Victory also crowned a strong week in Bogota as he won consecutive matches for the first time since undergoing double hip surgery in late January.
Tomic is also the first Australian champion in South America since Ken Rosewall triumphed in Buenos Aires in 1968.
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For Karlovic, it was a second defeat in a final against an Australian opponent in the space of a week after the 6ft 11in Croatian giant had been defeated by Lleyton Hewitt in the Newport decider last Sunday.
In what turned out to be a good weekend for Australian tennis, Sam Groth and Chris Guccione won the doubles title in Bogota.
He withdrew in the first round of this year's Australian Open against Rafael Nadal and underwent double hip surgery shortly afterwards and then suffered a record 26-minute defeat on his comeback event at Miami.
Last year, his father John was charged with assaulting his son's hitting partner, Frenchman Thomas Drouet in Madrid.