President Cyril Ramaphosa - championed as a graft-busting savior after his corruption-stained predecessor Jacob Zuma -- survived Tuesday's vote thanks to support from the African National Congress (ANC) that has ruled South Africa since the end of Apartheid.
Lawmakers voted 214 to 148 against proceeding with an inquiry that critics feared could politically destabilize Africa's most industrialized country.
The ANC holds 230 of the National Assembly's 400 seats.
But South Africa's opposition parties vowed not to let the case die, saying they would challenge the decision.
The African Transformation Movement, which tabled the motion that led to the creation of an inquiry panel that concluded Ramaphosa may be guilty of misconduct, said it would appeal to the high court in Cape Town on Monday.
"The decision by parliament not to investigate, we view that as irrational," party leader Vuyolwethu Zungula, told AFP.
"We are going to court to challenge the decision," he added.
The Democratic Alliance, the country's main opposition party, said it was weighing its legal and parliamentary options.
"We are not prepared to allow the matter to just simply go without any further exploration," party lawmaker Siviwe Gwarube told AFP.
Economic Freedom Fighters, a leftist group and the second largest opposition party, called for a "judicial review on an urgent basis" of the parliament's vote, dismissing the open ballot system as "flawed and characterized by fear."
The scandal began when a former spy boss filed a complaint with police in June, accusing Ramaphosa of having the burglars kidnapped and bribed into silence instead of reporting the matter to the authorities.
The president has not been charged with any crime and has denied wrongdoing. He did acknowledge the theft of $580,000 in cash that was stashed under sofa cushions at his farm -- a safer place, his employees said, than the office safe.