Friday's tremor that rocked the Kusasalethu mine, one of the world's deepest, with gold extracted at depths below 3 kilometres (1.8 miles), highlights the dangers of mining in South Africa.
"Search and rescue efforts will continue to recover the remaining two trapped employees," Harmony said in a statement.
South Africa is home to the world's deepest mines where workers operate at depths of up to 4 kilometres beneath the surface. The industry has reduced the number of miners killed, with a record low of 73 registered last year compared with 77 in 2015.
Kusasalethu, located 90 kilometres west of Johannesburg, has had a troubled history and been a flash point for labour violence and strikes in recent years, threatening its viability and underlining the social risks of mining in South Africa.