Responding to what it called "confusing reports in the media", spokesperson Thabo Masebe confirmed that South Africa was providing the aid to Zimbabwe.
This contravened the conditions of the aid that were outlined in September when the plan was announced.
According to the conditions, the R300m in aid was conditioned upon the successful formation of a unity government between Robert Mugabe’s Zanu-PF and the two factions of the Movement for Democratic Change.
Masebe said this was to ensure, "that the assistance reached the intended beneficiaries".
But as the situation in Zimbabwe has worsened, Masebe said that the food aid was necessary now.
"The aim is to provide urgent humanitarian assistance to circumvent a dire food security situation," said Masebe.
He said the aid would be released through new South African Development Community mechanisms that were announced last week.
"We are satisfied that the aid will reach the intended recipients in a non-partisan manner."
Masebe added that South Africa "remains committed to the establishment of an inclusive government".
Mugabe has been accused of using food aid as a political tool by limiting its distribution to areas that voted for the MDC in the March elections.