The organisation's secretary general, Salim Ahmed Salim, presented the money to Wednesday to Zimbabwe's ambassador to Ethiopia and permanent representative to the OAU, Neville Ndondo.
The natural disaster has caused such a crises of unprecedented magnitude and led to the loss of lives, rendering hundreds of thousands homeless, destroying farmlands and causing severe damage to infrastructure.
Ndondo said he appreciated the donation, adding that it was a very important gesture "particularly knowing the limited resources of our continent organisation."
Salim earlier in the week gave 500,000 dollars to Mozambique, which has been hit hardest by the floods currently carpeting southern African states.
He appealed for international support for Mozambique to help the country cope with an "overwhelming" humanitarian crisis.
Mozambican President Joachim Chissano said one million people have been affected by the floods as thousands continue to hang on to increasingly dangerous higher grounds, rooftops and tree-tops awaiting helicopters to rescue them.
Press reports expressed fear that the limited number of choppers used in the rescue operation might not manage to rescue all those cut off by the rising floods which have turned parts of southern Mozambique into a virtual sea.
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