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Cheika has been forced to reshuffle his back row.
Jaco Taute starts at full back in place of the injured Gio Aplon and Michael van der Spuy moves onto the bench, having last featured against the Lions in February.
"Players like Duane are the future of this union and it's an exciting opportunity for him to lead the team as we look to get back to winning ways now that we're back at home at Newlands."
The Australian international consequently missed last weekend's loss to the Sharks in Durban, but there had been hope that he would play some part against the struggling Stormers.
The halves are untouched with Nick Phipps and Bernard Foley in the playmaker roles.
You can see all the action from Newlands Stadium as the Stormers take on the Waratahs live on Sky Sports Xtra from 6.10pm.
Coetzee paid tribute to incoming skipper Vermeulen, who was a consistent performer for the team on their four match tour of New Zealand and Australia.
Replacements: 16 Coetzee, 17 Kebble, 18 Harris, 19 Fuzani, 20 Notshe, 21 Groom, 22 Catrakilis, 23 van der Spuy.
With Wycliff Palu ruled out with an ankle injury suffered in the loss to the Sharks in Durban, coach Michael Reebok Orange Sneakers
Captain Dave Dennis has been moved to number eight and Jacques Potgieter finds himself in his favourite spot in the back row.
Folau was rated 50 50 to take part in Saturday's game at Newlands after a blow to the throat two weeks ago in the Waratahs' win over the Rebels.
Vermeulen skippersFor the Stormers, No 8 Duane Vermeulen will captain the side in Saturday's clash in the absence of regular skipper Jean de Villiers, who will sit out this week with a meniscal cyst.
to think that Duane is just 27 years old, yet he has already played 68 matches for the Stormers and he continues to get better as a player and a leader," he told the Stormers' official website.
Damian de Allende starts in place of de Villiers at inside centre and Kobus van Wyk will take De Allende's place in the No 14 jersey.
Stormers v Waratahs
Waratahs: 15 Beale, 14 Alofa, 13 Ashley Cooper, 12 Lance, 11 Betham, 10 Foley, 9 Phipps; 1 Robinson, 2 Polota Nau, 3 Kepu, 4 Skelton, 5 Douglas, 6 Potgeiter, 7 Hooper, 8 Dennis (capt).
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Stormers: 15 Taute, 14 van Wyk, 13 de Jongh, 12 de Allende, 11 Tagicakibau, 10 Grant, 9 Schreuder; 1 Kitshoff, 2 Fourie, 3 Malherbe, 4 Botha, 5 Rhodes, 6 Carr, 7 Kolisi, 8 Vermeulen (capt).
the front row of Benn Robinson at loosehead, Sekope Kepu at tighthead and Tatafu Polota Nau at hooker.
Up front, Reebok Nano 6.0 Black meanwhile, the fit again Ruan Botha (ankle) takes the place of Jurie van Vuuren at number four lock in the only change to the pack this week, with Tazz Fuzani (on the bench) the only uncapped member of the match day 23.
Cheika has stuck solid with Saucony London Edition
With Potgieter out of the tight five, man mountain Will Skelton gets his chance and will start at lock alongside Kane Douglas.
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