Argentina's Del Potro breezed past Zemlja 7-5, 6-3, in the process avenging a title-match loss to France's Jo-Wilfried Tsonga in last year's Vienna final.
Del Potro notched his 12th career singles titles, adding to victories in Marseille and Estoril earlier this year.
The Argentine this year also reached the Rotterdam final -- where he fell to Roger Federer -- and collected a London Olympics bronze medal.
Zemlja had to get past No. 8 seed Xavier Malisse, No. 3 Tommy Haas and No. 2 Janko Tipsarevic before falling in his first ATP Tour final.