Duduzane, 35, had pleaded not guilty at a magistrates' court in Johannesburg to causing the death of Phumzile Dube after his Porsche hit a minibus.
One woman died in the crash, three others were injured and another passenger died in hospital weeks later.
Magistrate Tebogo Thupaatlase said the state had failed to prove the manslaughter charges beyond reasonable doubt.
"The accused is found not guilty," he said.
"None of the evidence presented established that there was anything that a reasonable man in the position of the accused, on that night would have foreseen."
Zuma had testified that his car had spun out of control after hitting a pool of water.
Amid tight security, former president Zuma was at the court to support his son, as well as Duduzane's twin sister Duduzile.
"The court assessed the situation well and the court's decision has made me happy," Jacob Zuma told reporters after the ruling.
Zuma, 76, was forced to resign in February 2018 over corruption allegations centred around the Gupta business family, who reportedly held such sway that they picked cabinet ministers.
Duduzane was previously employed by the Guptas.
Jacob Zuma, who has five wives and at least 20 children, has been charged with 16 counts of graft linked to an arms deal from before he became president.
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