Schalk Burger returns to the starting line-up at No 8, which sees Nizaam Carr moving back to the side of the scrum, while Siya Kolisi goes to the bench as Sikhumbuzo Notshe retains his place.
Fleck said after practice at Newlands on Thursday that Kolisi has been off the training field with flu this week, and that he didn’t want a similar situation that he experienced last week when he gave Frans Malherbe until match-day to get over his flu.
Malherbe pulled out, and it resulted in Damian de Allende suddenly being thrust into the captaincy role.
Burger, Notshe and Carr all have the ability to play towards the ball and neutralise the threat of Wallaby star opensider Hooper, who will captain the Waratahs on Saturday.
As expected, Juan de Jongh is back from his minor concussion to make his first appearance at outside centre in 2016, and it allows Fleck to field a Springbok combination alongside Damian de Allende.
The two other changes to the starting XV that beat the Reds 40-22 sees Malherbe taking over from Vincent Koch at tighthead, while JC Janse van Rensburg comes back at loosehead for Oli Kebble.
Johnny Kotze, who started at No 13 for most of the season, drops out of the squad altogether as Fleck feels that Brandon Thomson provides crucial back-up as a specialist flyhalf, while Huw Jones can play at centre, wing and fullback.
TEAMS FOR NEWLANDS
Stormers: 15 Cheslin Kolbe, 14 Kobus van Wyk, 13 Juan de Jongh, 12 Damian de Allende, 11 Leolin Zas, 10 Jean-Luc du Plessis, 9 Nic Groom, 8 Schalk Burger, 7 Sikhumbuzo Notshe, 6 Nizaam Carr, 5 Pieter-Steph du Toit, 4 Rynhardt Elstadt, 3 Frans Malherbe, 2 Bongi Mbonambi, 1 JC Janse van Rensburg.
Bench: 16 Scarra Ntubeni, 17 Oli Kebble, 18 Vincent Koch, 19 JD Schickerling, 20 Siya Kolisi, 21 Louis Schreuder, 22 Brandon Thomson, 23 Huw Jones.
Waratahs: 15 Andrew Kellaway, 14 Reece Robinson, 13 Israel Folau, 12 Kurtley Beale, 11 Rob Horne, 10 Bernard Foley, 9 Nick Phipps, 8 Jed Holloway, 7 Michael Hooper (captain), 6 Dean Mumm, 5 Will Skelton, 4 David Dennis, 3 Tom Robertson, 2 Hugh Roach, 1 Paddy Ryan.
Bench: 16 Tatafu Polota-Nau, 17 Jeremy Tilse, 18 Angus Ta’avao, 19 Sam Lousi, 20 Wycliff Palu, 21 Matt Lucas, 22 David Horwitz, 23 Matt Carraro.
Original source: Schalk back at No 8 for Stormers