Chad le Clos' second medal made the country proud of the swimmer, Mbalula said in a statement.
Le Clos snatched gold from Michael Phelps in the 200 metres butterfly final on Tuesday.
He added South Africa's fourth medal by tying second in the men's 100m butterfly in 51.44 seconds.
Mbalula commended Le Clos' gusty performance and praised the tightening of the qualification in ensuring that the country did not send "passengers" to the games.
"We invested lot of energy in ensuring our team is counted amongst the best in the world. The fact that we already bagged 3 gold and 1 silver medals dictate to us that we are on course" he said.
He urged South Africans to continue investing their time and energies in tweeting messages of hope and encouragement for the team and wear national colours.
Swimmer Cameron van der Burgh was the first to scoop the gold medal when he won the 100m breaststroke with a world-record time of 58.46 seconds. He was followed by Le Clos' with two medals.
South African rowing team made up of Sizwe Ndlovu, Matthew Brittain, John Smith and James Thompson snatched gold in the last few metres of the 2000m course to complete the four medals.