But with two minutes left on the clock South Africa were awarded a penalty try following Liam Williams' shoulder charge into Cornal Hendricks which Morne Steyn converted for the narrowest of victories.
The defeat was Wales 24th in 25 games against the southern hemisphere big three under coach Warren Gatland - the man in charge for the Lions successive tour down under last summer.
But while disappointed to see victory slip from their grasp, Jones insists it bodes well for the future.
"We are 15 to 16 months out from the World Cup, hopefully, this will send a bit of a flare up into the sky to say we are still here and hopefully we can be contenders," he said.
"We wanted to show fans we are not out here on a jolly. We wanted to put in a good performance."