The two teams were scheduled to meet in Queenstown on Sunday.
But a Covid-19 outbreak in Victoria this week, and a lockdown announced on Thursday, meant that was no longer possible after the New Zealand government extended their pause on quarantine-free travel from the state.
The Rebels had flown to Sydney on Wednesday, in the hope of then transferring to Queenstown.
But New Zealand's Covid-19 Response Minister Chris Hipkins said the team were covered by the travel pause because they were in Melbourne when it came into affect on Tuesday night.
The Highlanders would travel to Sydney on Saturday, with the match being played at Leichardt Oval.
"Fortunately, the Rebels were able to move out of Melbourne and relocate to Sydney on Wednesday and we're pleased to be able to play the match and chase the competition points," Highlanders CEO Roger Clark said.
New Zealand Rugby general manager of professional rugby Chris Lendrum said the health and safety of players and fans remained the number one priority for all parties.
"We are pleased to be able to keep the competition going, but are working closely with Sanzaar, Rugby Australia and the Rebels to ensure all measures are in place to keep the Highlanders players, coaches, and management safe.
NZR said all Rebels players and staff would be tested for Covid-19 before the match.
The Rebels were also continuing to check the locations of interest named by the Victorian State Government and, as it stood, no team members had been to any of the locations listed.
Clark said the club were disappointed for the people of Queenstown, fans, and the wider region, but grateful that the match could still go ahead.
"Our players and coaches were really looking forward to heading to Queenstown for what would have been a fantastic day and we share the disappointment of our fans that we won't be able to make it this season."
Meanwhile, the new Victorian lockdown could also affect the Chiefs hosting the Rebels in Hamilton next Saturday.
The lockdown was due to end less than 48 hours before the scheduled start of that match.