Mildred Oliphant announced the new minimum daily wage will "be pegged at 105 rand ($11.77, 8.68 euro) per day" from March, rising from 69 rand ($7.74, 5.7 euro) per day.
"I would urge organised business and labour in the agricultural sector to use this opportunity to come together to find ways of improving labour relations in their sector," Oliphant said.
The new wage will be introduced March 1.
Organised agriculture warned the 52-percent hike will force job cuts in the sector that employs approximately 700,000 people.
"What's going to happen now is that with the increase of labour costs we will actually go to a point now where we will shed surplus labour on the farms," said Carl Opperman of the Agri-Wes Cape, the regional commercial farmers union.
Workers went on strike in November over demands their basic pay be increased to 150 rands per day, described by farmers as unaffordable, which spread to several towns and killed three people.
The unrest in towns near Cape Town saw vineyards, property and vehicles torched and sparked several clashes with police firing rubber bullets.
A non-government report on the industry found the average wage on farms was around 85 rand and that if it increased to more than 105 rand, many farms would would be unable to pay operating expenses.
It also found that a wage of 150 rand would not provide the nutritional needs of workers.
The Food and Allied Workers Union described the raise as a "short term victory" for the workers, adding they will continue the fight for a bigger minimum wage.
"This raise of over 50 percent, by the department of labour, is a meaningful step towards obtaining a living wage for farm workers," the Food and Allied Workers Union said in a statement.
"We will, however, fearlessly continue to push for higher wages in the sector, with the clarion call for a R150 per day minimum as our mandate."
The wage hike comes on the heels of hefty wage increases won in the mining sector after the industry was rocked by wildcat strikes in which more than 50 people were killed.