The DMR issued the Section 54 order after an in loco inspection into the circumstances surrounding two separate fatal accidents on 17 and 27 May.
"The Section 54 order was lifted after the completion of a report back to the DMR, in terms of Section 11(5) of the Mines Health and Safety Act, on Friday evening, 30 May 2014, subject to the implementation of a number of specific remedial actions and instructions," the mine said in a statement.
It said that operations resumed in the Twin Shaft area with the commencement of the evening shift on Sunday evening and in the South Shaft area with the start of day shift this morning.
One of the deaths happened when a dump truck reversed over a contractor.
The other death was in a workshop where a 282 jumbo drill rig boom was being lowered. The boom was moved outwards and struck a man as he walked past.
CEO Nick Holland said on Friday that the mine will also have safety upgrades. He said it could take up to four months.
Following the lifting of the Section 54 order and the resumption of operations, the focus at South Deep for the next three to four months will be on the satisfactory completion of the secondary support backlog, with a view to returning the mine to normal production as soon as possible.
The South Deep mine has 4 000 employees and between 1 700 and 1 800 contractors, and Gold Fields is also talking to unions about possible job cuts, reported AP.
The National Union of Mineworkers said it was concerned about what it called a plan by Gold Fields to review 500 jobs at South Deep.