Swimmer Kirsty Coventry smashed the world record to win gold in the women's 200m backstroke and also captured three silver medals.
Mugabe handed the US-based swimmer the cash at a ceremony in Harare carried live on state television.
Mugabe said: "Our national spirit must exude joy and pleasure and say you have done well, daughter of Zimbabwe. We are proud of you, we wish you well. She's our golden girl ... take care of her."
The US dollars, scarce in a country struggling with an economic crisis marked by a severe shortage of foreign currency, were carried in a briefcase by Zimbabwe's central bank governor.
Other members of Zimbabwe's Olympic team received between $2 000 and $10 000 each.