The Highlanders bagged their first win of the season on Saturday night, beating the Sharks 25-22 in a nail-biter at Forsyth Barr Stadium.
They did it without Nonu, who is staying behind when the Highlanders take on the Kings and the Bulls in South Africa, and then the Force in Perth on the way home.
Nonu is nursing a sore knee, which has been troubling him all season.
''Ma'a has an injury that has not been right and we can't take guys that are not able to play. The good thing about Ma'a is that he played the first game and then got injured at training with a medial ligament,'' Joseph said.
''He missed the next two games. We lost, so the player [Nonu] felt compelled to come back and help the team. But he was not really helping himself, as his knee was not really right. That is the pressure he puts upon himself to contribute towards the team which is struggling.
''But he has always trained with a crook knee and that is not good for him, or the team. So we made a collective decision for him to have a breather and get it right.''
The other injury doubt was over utility back Phil Burleigh, who left the field on Saturday night.
It was touch and go whether Burleigh would recover in time for Sunday morning's (NZ time) game against the Kings in Port Elizabeth, so he has been left behind for a couple of days to be assessed.
If he does not recover soon enough, Trent Renata will fly to South Africa later this week. The Highlanders can take only 26 to South Africa under Sanzar rules.
It was a more buoyant team which boarded the plane yesterday afternoon, following its first win of the season on Saturday night, ending a run of 11 straight losses.
Joseph felt the Highlanders did not deserve to lose, but maybe a draw would have been a fairer result.
The execution from his side was more accurate and Joseph put that down to more confidence in the players, also pointing to the performances of halfback Aaron Smith and first five-eighth Colin Slade.
''At the start of the week we wanted to create real clarity and concentrate on the simple things. When you look at the so-called sloppy errors, I think that comes from guys not having confidence and going within themselves.
''You make a mistake and that compounds everything. So we have had to work our way out of that, albeit slowly. That has taken us eight weeks. I'm glad that has gone now and guys will hopefully have the confidence to win some games at this level.''
He praised the defence of his side at the end, as the Highlanders withstood a barrage from the Sharks.
''I put that down to desperation. The guys have copped a bit of flak, and rightfully so, I suppose, about not closing those tight matches. And I think that has resonated with a bit of attitude. We saw the players being desperate, backs against the wall.''
The Sharks went for a try at the end to win the game, as a draw would have been worth only two points, while another try and victory would have been five points.
In other games, the Blues beat the Stormers 18-17 and the Chiefs beat the Rebels 39-33. The Reds and Force drew 11-11, while the Waratahs smashed the Kings 72-10. The Bulls beat the Hurricanes 48-14 and the Crusaders beat the Brumbies 30-23.
Highlanders squad
For South Africa and Australia
Ben Smith, Tony Ensor, Hosea Gear, Tino Nemani, Jason Emery, Tamati Ellison, Phil Burleigh or Trent Renata, Shaun Treeby, Hayden Parker, Colin Slade, Fumiaki Tanaka, Aaron Smith, Elliot Dixon, TJ Ioane, Mose Tuiali'i, John Hardie, Joe Wheeler, Brad Thorn, Josh Bekhuis, Jarrad Hoeata, Chris King, Ma'afu Fia, Jamie Mackintosh, Tony Woodcock, Liam Coltman, Andrew Hore.
