ASA president James Evans said he was delighted with a solid performance after the team returned on Monday.
"By the last day of the championships [Sunday] I think the guys were just flat," Evans said.
"It took one and a half hours, on bumpy roads, just to get to the stadium each day.
"The food was bad and it was difficult to find decent drinking water.
"Some of the athletes were just overwhelmed by the circumstances, so considering the conditions, I think we did really well."
Eight athletes needed to set the Olympic qualifying standards one more time in their disciplines to reach the country's stringent criteria for the London Games ahead of the June 30 deadline.
Only Andre Olivier, who secured bronze in the men's 800 metres, was able to set the required mark in his event at the continental championships.
Olivier is expected to be included in South Africa's final Olympic team, which will be announced on Wednesday.
"Conditions were always going to be difficult to qualify," Evans said.
"We're just hoping that Sascoc [the South African Sports Confederation and Olympic Committee] will take position into account, not just times, and consider guys who just missed out."
The South Africa team bagged 24 medals in Benin – six gold, 10 silver and eight bronze – to finish behind Kenya and Nigeria in the medals table.
They were spearheaded by sprinter Simon Magakwe who won gold in the men's 100m and 4x100m relay.
At the 2010 edition of the biennial African Championships in Nairobi, Kenya, South Africa had also finished third, though they returned home with only 19 medals – five less than they earned in Benin.
"If you consider that Nigeria is an hour's drive from Benin, so they are used to the conditions – and they took a really big team – we're pretty happy," Evans said. – Sapa