Co-captains back for Stormers
De Jongh takes his place at outside centre after missing the 40-22 victory over the Reds last week with concussion, and will partner Damian de Allende in midfield, while Malherbe returns at tighthead prop after being ruled out last week due to illness.
The only other changes to the starting line-up are rotational switches to the forward pack as Schalk Burger takes his place at No.8 with Nizaam Carr shifting to the flank and Siyamthanda Kolisi moving to the replacements bench, whilst in the front row JC Janse van Rensburg starts at loosehead prop.
Stormers head coach Robbie Fleck said that his team are intent on raising the bar once again at Newlands.
"We are determined to keep on progressing along the path we have embarked on this season, and the Waratahs will provide another serious challenge this weekend.
"The team has really bought into what we are trying to do, and I am excited to see what they can produce in front of our faithful fans on Saturday," he said.
Stormers: 15 Cheslin Kolbe, 14 Kobus van Wyk, 13 Juan de Jongh (co-captain), 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 (co-captain), 2 Mbongeni Mbonambi, 1 JC Janse van Rensburg.
Replacements: 16 Siyabonga Ntubeni, 17 Oliver Kebble, 18 Vincent Koch, 19 JD Schickerling, 20 Siyamthanda Kolisi, 21 Louis Schreuder, 22 Brandon Thomson, 23 Huw Jones.
Date: Saturday, April 30
Venue: Newlands, Cape Town
Kick-off: 19.15 (17.15 GMT: 03.15 AEST, Sunday, May 1)
Referee: Mike Fraser (New Zealand)
Assistant referees: Paul Williams (New Zealand), Cwengile Jadezweni (South Africa)
TMO: Shaun Veldsman (South Africa)