The hosts played an energetic hard-running game against a steely Malian defence and were unlucky not to find the net on more occasions.
Speaking after the game Gordon Igesund told reporters of his admiration for his team's performance saying that Bafana Bafana showed the requisite amount of passion to beat Mali.
"My boys lost with dignity, pride and passion. There is only so much any coach can ask from his team and my boys gave everything they had," Igesund said.
South Africa was threatening throughout the first half and looked set to record a famous win after Tokelo Rantie's tap in, but Mali was able to get back into the game after Seydou Keita headed in from close range.
The remaining period of the match saw both sides apply pressure but penalties had to determine the winner after 120 minutes of hard-fought football.
"It is very difficult to accept defeat when you play so well. Congratulations to Mali for winning a tough game for both teams," Igesund concluded.
Mali coach Patrice Carteron also spoke of South Africa's attacking prowess in the opening period but praised his player's patience after the match.
"The South Africans posed a lot of problems in the first half and we had to change the tactics in the second half to get back into the match," Carteron said.
"They pressed us with a lot of diversity. But we knew we had to be patient and we had time to fight back."