The Afcon group stage matches were concluded on Wednesday when Ivory Coast and Togo progressed to the quarter finals after eliminating Algeria and Tunisia.
"As we concluded the group stages, we can announce that ... Afcon ... has been a great success. Even in areas where we started with poor match attendance at the stadiums, this has improved over time.
"We attribute that to the ever passionate, enthusiastic fans and display of football from all the 16 participating nations, including those who have been eliminated," Mbalula told reporters on Thursday in Johannesburg.
"South Africans, as always, have been good hosts," he said.
Mbalula commended law enforcement agencies for having swiftly dealt with the clash between DR Congo and Ghana fans at the Nelson Mandela Bay Stadium in Port Elizabeth.
In another incident, an Ethiopian fan, who allegedly invaded the pitch when his team was losing in Mbombela, was also immediately arrested.
He thanked visitors from the participating nations for the vigour displayed in their support of the tournament.
Mbalula also congratulated tournament debutants, Cape Verde, who made history by reaching the quarter finals of the continental showpiece.
With regard to Bafana Bafana, who will face Mali in the quarter finals at the Moses Mabhida Stadium on Saturday, Mbalula said: "The national team players should understand that as a nation, we've won the battle not the war. Our strategic objective is to win the war.
"Our boys are well on track to realising that we are playing opponents who can equally upset us and we want to wish them good luck on their upcoming match against Mali."
As South Africa was booted out of the quarter finals by Mali when they hosted the tournament in 2002, Mbalula said Bafana should use Saturday's match as an opportunity to make the nation proud.
Safa President Kirsten Nematandani urged South Africans to continue rallying behind the national team.
"We need to thank South Africans who always come to the stadium in great numbers to support the national team, and I believe this makes the boys have an everlasting fighting spirit.
"We want to once again urge South Africans to fill up Moses Mabhida Stadium to capacity as their unwavering support will inspire the players to win."
Nematandani said the mood at the Bafana camp was very spirited and driven, and the players were looking forward to their encounter with Mali.
The Passenger Rail of South Africa (Prasa) has set aside 20 trains with a capacity to support 40,000 fans at a time.
In KwaZulu-Natal, Prasa has set aside 26 trains to transport fans to all the games taking place at the Moses Mabhida Stadium.
Prasa has decided to run a special Shosholoza Meyl train from Johannesburg to Durban for the quarter final match on Saturday.
The train will depart from Park Station in Johannesburg at 0620 today, and it will arrive in Durban at 0830 tomorrow. It will return to Johannesburg on Sunday.
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