Jonathan Bornstein was born on November 7, 1984 in Torrance, California. The members of his father's side of the family are Jewish descendants of Romania and his mother is Mexican. He attended Los Alamitos High School where he played soccer all four years. He started his college soccer career at Cal Poly Pomona and transferred after two years to UCLA, where he was roommates with future national teammate Benny Feilhaber.
In 2006, he was taken by Chivas in the fourth round of the 2006 MLS SuperDraft. The same year he won the MLS Rookie of the Year Award. In July 2010, it was announced by Chivas USA that Bornstein would be joining Tigres de la UANL in the Primera División de México in 2011, following the conclusion of the 2010 Major League Soccer season.
After sitting out the first two group-stage games for the United States in the 2010 FIFA World Cup in South Africa, Bornstein started at left back against Algeria in the final group play game and against Ghana in the round of sixteen.