"By show of hands, we have a majority and the withdrawal carries. The resolution will be withdrawn," DA federal chairperson Wilmot James told delegates in Boksburg on Sunday.
The congress originally resolved to change the party's stance on the process from opposing to supporting fracking.
The withdrawal of the resolution means the DA's original stance of being fundamentally against fracking until stringent control measures were put in place remains.
But the DA's spokesperson for mineral resources, James Lorimer, downplayed the consternation over the failed resolution, arguing it was mere "semantics".
"We have never been anti-fracking and we remain that way," Lorimer told the Mail & Guardian.
Western Cape minister of transport and public works Robin Carlisle told the congress earlier in the day: "Fracking must happen, but … in a responsible way."
While resolution 24 originally proposed no fracking until certain conditions were met, it was changed to the party being in full support of the process provided conditions were met.
This move by the opposition party followed a September decision by Cabinet to drop a moratorium placed on the process.
A number of gas and oil companies, including Shell, Falcon Gas and Oil, and Sasol had applied for prospecting rights over areas of the Karoo when the department of mineral resources instituted the moratorium last year.
Fracking uses a mixture of sand, chemicals and vast quantities of water to release shale gas reserves trapped underground.
Gas is seen by many, including South Africa's national planning commission, as a means to bridge the country's electricity supply shortages.
Critics fear the process of fracking will contaminate water supplies in an already dry area, and damage air quality.
Lorimer said the DA could not ignore the potential job creation and economic development that could be enjoyed through fracking.
"We cannot be seen to be against the prospect of massive job creation and economic opportunities for the people of South Africa," he said.
Lorimer also argued there was added pessimism directed towards fracking based on the current government's performance.
"This government has a terrible record of economic and environmental stewardship."