Zuma called the ruling groundbreaking and said he respects it without reservations.
"The judgment underscores the values that underpin our hard-won democracy," Zuma said, while still insisting he didn't act dishonestly.
His remarks to the nation came a day after the court ruled he defied the South African Constitution
with his use of government money to renovate his home in Nkandla, a controversy that dates back to his first term nearly seven years ago.
The upgrades included adding a swimming pool, cattle enclosure, chicken run, visitors center and amphitheater.
Zuma was ordered to repay money on renovations unrelated to security. The National Treasury will determine exactly how much.
"The constitution, rule of law and accountability is the sharp and mighty sword ready to chop off the ugly head of impunity," the court ruled Thursday.
The court also faulted the National Assembly for its investigation of the President, saying its exoneration of him "was inconsistent with the Constitution and unlawful."
Even as he accepted the court's decision, Zuma said Friday he did "never knowingly or deliberately set out to violate the constitution, which is the supreme law of the land."
"The matter has caused a lot of frustration and confusion for which I apologize on my behalf and on behalf of the government," he said.
"I ask all parties to respect the judgment and abide by it. Let us use the judgment to build and further strengthen our democracy."