The flyhalf was one of a trio of experienced British and Irish Lions drafted in to start Wales's third group match and give the frontline players a rest.
Jones, who has recovered from a calf injury, will make his debut at his fourth World Cup and move ahead of Gareth Thomas as his country's most-capped player.
Former Wales skipper Ryan Jones has also recovered from a calf problem and comes into the team at blindside flanker for his first taste of World Cup action after missing the 2007 tournament through injury.
Prop Gethin Jenkins will make his 78th appearance for Wales against the Namibians in a side that features 11 changes from the team that beat Samoa 17-10 last week.
"On the back of two tough and intensely physical matches we have been able to make some changes to the squad, but also bring a lot of experience into the side at the same time," Wales coach Warren Gatland said in a news release on Saturday.
"Stephen, Ryan and Gethin in particular bring a wealth of experience but we have some previously established combinations elsewhere in the side as well, in the second row, the midfield and at halfback, so we are excited and looking for this side to do well against Namibia."
The Welsh, who narrowly lost to South Africa in their opener before edging Samoa in a bruising encounter last week, will be confident of a comfortable victory in New Plymouth over a Namibian team who lost 87-0 to the Springboks on Thursday.
"They will be hurting after their loss to South Africa, but we will be concentrating on ourselves and our own performance," Gatland added.
"This is the rugby World Cup and every performance counts, we showed great heart and courage last week to grind out a win and this week we need to do similar, but also improve and take that next step towards qualification from this incredibly tough group."
The Welsh face Fiji in their last pool clash on Oct. 2.
Team: 15-Lee Byrne, 14-Leigh Halfpenny, 13-Jonathan Davies, 12-Scott Williams, 11-Aled Brew, 10-Stephen Jones, 9-Tavis Knoyle, 8-Toby Faletau, 7-Sam Warburton (Captain), 6-Ryan Jones, 5-Alun Wyn Jones, 4-Bradley Davies, 3-Craig Mitchell, 2-Lloyd Burns, 1-Gethin Jenkins.
Replacements: 16-Ken Owens, 17-Ryan Bevington, 18-Luke Charteris, 19-Andy Powell, 20-Lloyd Williams, 21-Rhys Priestland, 22-George North.