They were killed as they reported for work at Lonmin's strike-hit platinum mine, threatening the firm's plans to end the industrial action this week.
Lonmin, the world's no.3 platinum producer, was hoping miners would start returning this week after the company took its wage offer directly to employees, sidestepping the AMCU union in a bid to end its four-month strike.
"Two mine workers were killed this morning. NUM members who went to work are being intimidated and assaulted," NUM spokesman Livhuwani Mammburu said.
Lonmin's chief executive confirmed one employee was killed, but provided no other details on a conference call with reporters.
The Solidarity union, which mainly represents skilled workers, also said its members at Lonmin were being intimidated.
Lonmin's larger rivals, Anglo American Platinum and Impala Platinum, have also presented wage offers to employees after talks with the Association of Mineworkers and Construction Union (AMCU) collapsed.
The strike is the longest and costliest to hit South Africa's mines, highlighting the discontent among black miners who feel they are still not reaping the benefits of the country's mineral wealth two decades after apartheid ended.
It has hit 40 percent of global platinum output and dented already sluggish growth in Africa's most advanced economy.