The side is due to land in South Africa this morning without Smith, who is nursing a sprained ankle. The All Black fullback is back in Dunedin, though he may head to Perth and play against the Force on May 20.
Smith picked up an ankle injury in the opening minutes of the game against the Stormers last Friday night but managed to battle on through the 80 minutes.
Highlanders coach Tony Brown was confident straight after the game his captain would get on the plane but in the end the decision was made to leave him at home.
Highlanders chief executive Roger Clark said yesterday it was decided Smith would stay in New Zealand to rest his injury.
Provided the ankle came right and he was declared fit, Smith would head across the Tasman to play against the Force.
Tevita Li came into the squad to head to South Africa.
The side had plenty of options at fullback, with Richard Buckman and Matt Faddes able to play in the position.
With a long season looming ahead for Smith, with both the Highlanders and the All Blacks, it was wiser to get the injury right rather than carry it into a long plane flight and play in South Africa.
Smith has his ankle in a moon boot but these days players tend to get them fitted even if they clip a toe nail so it does not mean the injury is overly serious.
One bonus for the Highlanders was if Smith plays against the Force he will be able to play his record-breaking 128th game for the franchise at home, against the Waratahs on May 27.
All players who went on the flight to South Africa will be available for the first game.
Hooker Ash Dixon will make his 2017 debut for the team provided he is selected against the Cheetahs in Bloemfontein early Saturday morning (NZ time). He has recovered from a back injury he picked up in pre-season and could captain the side.
Loose forwards Elliot Dixon (knee infection) and Luke Whitelock (concussion) both headed to Africa having got over their issues.
Injured All Black first five-eight Lima Sopoaga may be a chance to play against the Force. He has been out since March 11 with a hamstring injury but could play club rugby this weekend.
Flanker Dan Pryor may also play his first game for six months this weekend in club rugby to test his repaired knee.
The side will base itself in Johannesburg for the two games in Africa, playing the Bulls in Pretoria on May 14 following the game in Bloemfontein.
The Highlanders should go into their next game full of confidence after beating the Stormers 57-14. In other games over the weekend, the Chiefs beat the Sunwolves 27-20, the Waratahs beat the Reds 29-26, the Lions beat the Force 24-15, the Crusaders beat the Cheetahs 48-21, the Kings beat the Rebels 44-3 and the Sharks beat the Jaguares 33-25.
In Canberra last night, the Blues beat the Brumbies, 18-12.