The consignment - the largest of its kind to be trafficked through a South African port of entry - was discovered during a routine inspection of the airport's cargo area said police spokesman, Captain Dennis Adriao.
"The team of SAPS members from the anti-smuggling unit routinely search the cargo areas for drugs and illegal items," said Adriao.
In addition to the counterfeit DVDs, a consignment of counterfeit DVD players, as well as cellphones and Dolce & Gabbana clothing was found.
Police were still busy with an inventory of the second consignment on Wednesday afternoon.
It is believed that the two consignments came to South Africa from China, via Dubai.
"The syndicates are very cunning - the two consignments were destined for Nigeria and we believe that the goods would have come back into South Africa via Nigeria," said Adriao.
Police believe that the planned route was an attempt by the syndicate to avoid detection by South African authorities.
A suspect in Nigeria has been identified and Adriao said that South African authorities would be working with international law enforcement agencies to bring those involved to book.
"Depending on the quantity of the counterfeit goods, one could be looking at quite a lengthy prison sentence," he said.
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