It was enough for Moir to rise from fifth in the standings to the top spot.
The riders now have seven weeks to regroup for the three North Island rounds to follow, starting with Hampton Downs, near Huntly, on March 2-3.
Alastair Hoogenboezem, of Christchurch, remains second in the Superbike standings, 17 points behind Moir, with Wellington's defending Superbike champion Sloan Frost improving from eighth to third.
Rees has slipped from first to fourth in the standings, but he is just three points behind Frost.
In the Supersport 600 class, the championship finally got under way after racing was abandoned at Ruapuna due to an oil spill. However, organisers made up for it with an extra race in the programme in Timaru.
Manukau's Toby Summers ended was most dominant in Timaru, winning three of the four Supersport 600 races. He crashed out of his other race, but still had enough points to top the podium.
Second in the overall standings for the class is Rangiora's Avalon Biddle, who showed that consistency counts for plenty. Her 3-4-2-3 scorecard for the weekend put her just ahead of Tapanui's Seth Devereux in third.
Devereux crashed out of race one but followed that with 2-1-2 finishes.
"I'm riding well at the moment and feeling confident," Summers said.
"These South Island tracks seem to suit my aggressive style. Hampton Downs coming up is not my favourite track, but I'm still looking forward to the races there."
Other class leaders after the weekend's event are Palmerston North's Jacob Stroud (Supersport 300 class), Papamoa's Leon Jacobs (250 Production class), Jacob Stroud and Chris Huddleston equal first (in Superlites), Christchurch's Andrew McLaughlin (650 Pro Twins, provisional only), Australia's Yanni Shaw (125 GP), Hamilton's Jesse Stroud (GIXXER Cup, provisional only), Christchurch's Dennis Charlett and Will Clim (sidecars).
Meanwhile, Timaru's Harry Parker won the Allan Ramage Memorial Trophy, topping the points ahead of Jacob Stroud and New Plymouth's Hayden Lockhart in the separate series of three quick fire races.
Entries for the Allan Ramage Memorial were by invitation only, comprising the fastest 12 qualifiers from the 300cc and 250cc groups.
After round three at Hampton Downs in March, the nationals continue on in Manawatu on March 30-31, before wrapping up in Taupō on April 5-7.
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