Opposition parties had hoped the secret vote would mean MPs from the governing African National Congress (ANC) might side with them against the president.
But the motion, called amid repeated allegations of corruption, was defeated by 198 votes to 177.
This news was greeted with cheers and singing by ANC MPs.
Pro-Zuma supporters celebrate in Cape Town
In order for the no-confidence motion to pass, at least 50 out of the ANC's 249 MPs would have had to vote against the president.
However, the result does mean at least 26 ANC MPs rebelled, while another nine MPs abstained from voting.
Earlier, opposition MP Andries Tlouamma, deputy president of the Agang party, warned that if Mr Zuma survived then South Africa was "on a highway to hell".
Meanwhile, the Democratic Alliance's Mmusi Maimane said: "Today our choice is between right and wrong; between good and evil."