Flanker and captain Michael Hooper, prop Sekope Kepu, lock Rob Simmons, flyhalf Bernard Foley and fullback Kurtley Beale will be left in Australia as part of a World Cup rest policy struck with Wallabies coach Michael Cheika in the off season.
The Waratahs, champions in 2014, still have an outside chance of qualifying for the postseason but need to beat the Highlanders handsomely in Dunedin and hope a slew of other results go their way.
Waratahs coach Gibson said last week he would not guarantee any of his top players would be rested for the final round but duly followed through on his deal with Cheika in his squad released on Wednesday.
Flyhalf Mack Mason comes in for Foley, with Will Miller to replace Hooper and regular blindside flanker Ned Hanigan slotting into the second row.
Facing a weakened Waratahs side will boost the Highlanders' slim hopes of keeping their own season alive as they look to claim one of the four remaining wildcard berths up for grabs.
The Highlanders are on 31 points, one ahead of the Waratahs, and need a bonus point win over the Sydney team. Even then, they need other results to go their way.
Co-captain and fullback Ben Smith will have to farewell fans from the sidelines after he lost his race to recover from a troublesome hamstring.
The All Blacks veteran is leaving New Zealand to play in France after the World Cup in Japan.
“Ben worked extremely hard to be available for his team this week, unfortunately he is still a little short of being match ready," coach Aaron Mauger said.
(Reporting by Ian Ransom; Editing by Peter Rutherford)
