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Van der Merwe, who missed their last two matches with a groin injury, replaces Wilhelm Steenkamp at lock.
Steenkamp moves to the bench where he replaces England-bound Gerrit-Jan van Velze.
In another swop, fit-again Dean Greyling moves back into the number one jersey, with Dawie Steyn, who debuted against the Brumbies in their last match two weeks ago, missing out altogether.
On the bench, Willie Wepener is also back in the fray after recovering from a facial nerve infection, replacing Bongo Mbonambi.
Deon Stegmann was close to selection, but Ludeke felt the specialist fetcher needed some time on the training paddock first to get into the team patterns again.
"We need to start well and everyone is aware of that," Ludeke said.
"The Rebels are one of those teams who refuse to go away and we will need to play for 80 minutes to beat them.
"We have travelled well and in good spirits, so we are keen to play."
Bulls captain Pierre Spies said they were eager to get their Australasian tour off to a positive start.
"This is a new venue for us and the importance of getting the tour under way with a positive performance makes everyone very keen to get out there," Spies said.
"The Rebels challenge you with good scrambling defence and have playmakers all round, so we need to focus on our strengths for this one."
Teams:
Rebels:
TBA
Bulls: 15 Zane Kirchner, 14 Akona Ndungane, 13 JJ Engelbrecht, 12 Wynand Olivier, 11 Bjorn Basson, 10 Morne Steyn, 9 Francois Hougaard, 8 Pierre Spies (captain), 7 Jacques Potgieter, 6 CJ Stander, 5 Flip van der Merwe, 4 Juandre Kruger, 3 Werner Kruger, 2 Chiliboy Ralepelle, 1 Dean Greyling
Substitutes: 16 Willie Wepener, 17 Frik Kirsten, 18 Wilhelm Steenkamp, 19 Arno Botha, 20 Jano Vermaak, 21 Louis Fouche, 22 Johann Sadie
