The Scarlets fly-half has not played since pulling out during the warm-up before Wales' opening World Cup preparation game against England at Twickenham a little more than four weeks ago.
Jones, who needs one more appearance to break Gareth Thomas' Wales cap record of 100, is battling with James Hook for the number 10 shirt.
"Steve has continued to do his rehab," said Howley, of Jones' calf muscle injury. "He hasn't taken a full part in training as of yet, and hopefully he will take a full part probably tomorrow.
"At this moment, obviously there is a doubt.
"He hasn't played for a long period of time. We need to give Steve enough time to make sure he is right. We are giving him plenty of time."
Wales coach Warren Gatland is due to announce his starting line-up on Friday for a game that will put the winners in pole position to claim Pool D's top spot.
"In a World Cup it is about winning and gaining momentum," added Howley.
"All we are looking ahead at is the game on Sunday, which is so important to us.
"It's about making sure we play in the right areas. Some of our players have played against South Africa eight times over the last three or four years, including their Lions experiences in 2009.
"The players have learnt, and that is what Test match rugby is about."
Wales team manager Alan Phillips, meanwhile, has maintained the squad's upbeat mood building towards Sunday's clash.
"It is the right time for us to play them, but we will never lose sight of the fact that they are a formidable outfit," said the former Wales hooker.
"The results have been close the last few times we have played them, and that is going to help our confidence."
And Phillips has identified Wales' punishing summer training camps in Poland as critical during a tournament build-up which also featured victories over England and Argentina.
"There is no doubt the training in Poland helped us, not just physically, but mentally as well," he added. "It toughened up our squad. We tried to break them (players), but they kept coming back for more.
"After that, the big bonus for us was the summer results because they helped boost our confidence. There is no doubt this squad believes they can do something special.
"There is no doubt that if we start playing well we will just start getting better and better."
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