But a vastly improved performance in the second Test, which was lost 37-21 at Loftus Versfeld, gave the hosts a scare and helped atone for the shambles in Bloemfontein.
South Africa, New Zealand and Australia await in the November internationals and Jones wants Wales to prove what they are capable of against the Tri-Nations big guns.
"Overall the second Test was a huge improvement and we're happy with that. We showed what should have been," he said.
"Hopefully now we'll go on to display our true character. We had the belief last week that we could win but that didn't translate onto the pitch.
"You can't look at defeat as redemption and we're bitterly disappointed not have won one of the Tests.
"But we've proved to South Africa as well as ourselves that we are a successful squad with a lot of potential.
"We've learned that we need to have a lot more confidence in ourselves.
"South Africa are the world champions and we did well in the Six Nations. After 60 minutes yesterday there was nothing in it.
"Hopefully we've gained their respect. They're a proud rugby nation like ourselves. We didn't do ourselves justice but we can hold our heads high leaving the country."
Assistant coach Shaun Edwards believes Wales are only a try behind the Springboks in standard and was pleased with the way his players responded to their drubbing at Vodacom Park.
"The guys have proved to me that they don't give in. Resilience is a great thing for any team or sportsperson to have," he said.
"After what happened in the first Test some teams would have felt sorry for themselves but we didn't.
"Some of the guys were working on their computers at 7.30am the morning after the first Test, that's how disappointed they were.
"The second Test was a fairer reflection of how good this team is. A five-point win by the Boks is where we're at right now.
"We're on a journey to being competitive against the southern hemisphere and beating them on occasion."