Del Potro, who won four tournaments last year - two on clay and two on hard courts - broke Querrey's service in the ninth game of the second set and then held serve to close out the match.
Querrey was attempting to win his second career ATP tournament after capturing his first title last year at Las Vegas.
The top-seeded team of Martin Damm of Czech Republic and Robert Lindstedt of Sweden beat No. 2 Scott Lipsky of the United States and Leander Paes of India 7-5, 6-4 in the doubles final.
It was the 36-year-old Damm's 38th career doubles title, while Lindstedt has four.
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Del Potro, Querrey reach Auckland semis
