Spokesman John Kirby maintained the payment was negotiated separately from the release, but said it was withheld until the Americans had left Iran.
Five Americans held in Iran were released in January in exchange for seven detained Iranians.
The US airlifted $400m (£300.8m) worth of cash to Iran on the same day.
The exchange came as the US lifted international sanctions against Iran as part of the country's historic nuclear deal.
The timing of both incidents has prompted an outcry from Republicans, who accused the Obama administration of quid pro quo.