The winter friendly was part of the US preparation for their upcoming 2010 World Cup qualifier against Mexico.
Kljestan, 23, scored in the 17th, converted a penalty in the 40th and completed his hat trick in the 74th – notching his first three international goals.
Kljestan, who had two goals for the United States at the Olympics in Beijing, opened the scoring by firing a free kick over the wall and past Swedish goalkeeper Johan Dahlin.
After Marvell Wynne was tripped inside the penalty area, Kljestan took the penalty kick and beat Dahlin to give the hosts a 2-0 advantage.
Daniel Nannskog cut Sweden’s deficit to 2-1 in the 73rd minute, but Kljestan responded a minute later, taking a pass from Brian Ching and firing home with his left foot.
Mikael Dahlberg added another goal for Sweden in the 89th minute, heading a
cross past US keeper Troy Perkins.
The match was a tune up for the United States ahead of their World Cup qualifying clash against Mexico, which will be played in Columbus, Ohio, on February 11.
Sweden will take on Mexico in another friendly next Wednesday in Oakland, California, before heading home to continue World Cup qualifying in Europe.