Slipper was a notable absentee when the Brumbies unveiled their squad for Saturday night's crunch clash with the Western Force in Perth.
The 34-year-old injured his calf in last week's 53-17 win over the Rebels in a setback that pits him in a race against time to be fit for the finals, which start next week.
The severity of Slipper's injury is yet to be revealed.
The Brumbies (48 points) are guaranteed to finish in the top four, and could snare top spot if they beat the Force and both the Blues (51 points) and Hurricanes (51 points) lose.
Blake Schoupp, who has recovered from a shoulder injury, has replaced Slipper.
The Force have been boosted by the return of former Wallabies lock Sam Carter from a hamstring injury.
But the news has been offset by a groin niggle to five-eighth Ben Donaldson, who has been replaced by Max Burey.
For the ninth-placed Force to have a chance of snaring a finals berth, they need the Melbourne Rebels to beat the eighth-placed Fijian Drua in Lautoka on Saturday.
Despite having a maiden finals berth locked away, the seventh-placed Rebels have opted against resting any players for the clash as they try to wrestle back some winning momentum after five consecutive losses.
With his foul-play charge dismissed, ex-Reds prop Taniel Tupou will play his 100th Super Rugby match, while the Gordon brothers - Carter and Mason - will start together for the first time.
Mason, 21, will make his starting debut at fullback, with regular 15 Andrew Kellaway shifting to the wing.
The Queensland Reds will finish fifth regardless of the result in Friday night's match against the hapless Waratahs.
Joe Brial and Connor Vest will start at No.8 and lock respectively for the Reds, while coach Les Kiss has managed workhorse second-rower Ryan Smith and prop Jeffery Toomaga-Allen.
Lawson Creighton has been named at No.10 and Tom Lynagh will come off the bench, but there was no room for winger Suliasi Vunivalu, who was free to play after serving a one-match suspension.
James O'Connor will receive some much-needed game time at club side Brothers after playing just 69 minutes across three bench cameos in an injury-hit season.
Brial's childhood was split between Queenstown and Sydney.
The 22-year-old holds the rare achievement of playing for both the Junior Wallabies and New Zealand Under-20s.
There is a significance to facing the Waratahs, the side that father Michael captained en route to playing for the Wallabies in the 1990s.
"It's unreal to get this first start in Sydney against the Waratahs," the 114kg Brial said.
"It's a great feeling. The games I've played off the bench have shown me I'm ready for it at this level."
Former Wallabies prop Paddy Ryan has answered an SOS call from departing Waratahs coach Darren Coleman, who is still dealing with an injury crisis to his front row.
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