Zuma was responding to a question from DA parliamentary leader, Lindiwe Mazibuko, about wage negotiations at Lonmin mine, Sapa reported.
Mazibuko had asked if he would consider changes to the labour relations regime, which pegged the union representation threshold at 51%.
She said this had led to the situation where AMCU (the Association of Mineworkers and Construction Union) was not a recognised union at Lonmin's platinum mine, and therefore excluded from wage negotiations.
Zuma said that within a democracy the majority prevailed.
"We operate within regulated society... Between workers and employers there have been negotiations and agreements, and those agreements must be respected," Zuma said.
"In a democratic situation, it is the majority that prevail. I can't change the rules because you want to make a particular point. You can't then say, smaller unions must then be compared to the bigger unions in the same way."
The president said workers who did not join the majority union could not expect the same privileges.
"You have more rights because you're a majority; you have less rights because you're a minority. That's how democracy works," he said, provoking a huge outcry from opposition benches.
Zuma told MPs it was "a question of accepting the rules of democracy, and operating within them".
An unidentified MP responded from the opposition side of the House: "You don't understand democracy!"