The dispute triggered a sharp market reaction when it was first disclosed in April, with Aspen's shares plunging more than 30% the day after it issued a profit warning citing the disagreement with a contract manufacturing customer.
The company also warned that normalised earnings from its manufacturing business could be R2bn lower than previously guided.
Aspen said at the time that the dispute had come "from left field" and was not known to management during its March interim results presentation.
It flagged potential implications for its French sterile manufacturing site, a key driver of profitability in its half-year earnings.
Aspen did not name the counterparty involved, but said the payment, due by 1 December this year, resolves the matter in full and final settlement.
Its shares were up more than 2% at 12.31 GMT.
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