Racing his 6.2 litre, alloy V8-powered Corolla, he finished third in the one-hour series, two laps behind winner Auckland's Hugh Gardiner in his Porsche GT3.
Runners-up Hayden Knighton and Garry Cliff, of Christchurch, were also driving a GT class car, a Porsche GT3 997, which left Henderson the winner of class one.
As the German marque dominated the three-hour series podium, Henderson's car was the only non-Porsche to place in the overall top three in both series.
Henderson said his Toyota was built entirely in his Midway Motors car yard workshop.
''I tell you what, the boys put a lot of hours into it. It makes it more of a team sport.''
Dunedin's Warren Good took his BMW to third in the one-hour series' class two.
Over in the three-hour series, Dunedin's Allan Dippie and his Invercargill co-driver, Scott O'Donnell, recovered from a spin on the first lap to finish fourth in their Porsche GT3 Cup S.
O'Donnell said on the SIES Facebook page it was ''another tough day at the office for our team.''
''Punted off on the first lap which removed the front splitter. Five laps to fix it. Happy with fourth given our lap-one drama.''
Andrew Bagnall and Ant Pedersen won the opening round in a Porsche 997 GT3, holding off the fast-finishing Porsche of multiple series champion Paul Kelly and co-driver Craig Baird by 4.377sec.
The Kelly/Baird Porsche was gaining three seconds a lap in the closing stages after a safety car intervention but ran out of time to hunt down the Bagnall/Pedersen Porsche.
Third place went to the Auckland and Australia-based pairing of Sam Fillmore and Danny Stutterd in a Porsche.
Alexandra's Bruce Davidson and Dave Garden had high hopes when they qualified their home-built Corvette C6R into third on the start grid. However, they spent close to half the race in the pits trying to rectify a brake problem.
Prominent non-finishers included the Craig Innes/Simon McLennan Porsche, the Matt and Dwayne Carter Falcon V8 Supercar, which had alternator problems, and the Robin Gray/Jono Lester Ferrari F430, which broke an exhaust manifold.
The much anticipated debut of Southland's Inky Tulloch, co-driving with Queenstown's Grant Aitken in his newly imported Camaro GT3, did not occur, due to the electronic management system malfunctioning in race mode.
In the class 3/4 battles, Otago drivers featured with Paul Coghill (Dunedin)/Kynan Yu (Cromwell) second in a Honda Civic Type R ahead of class regulars Ken Sinclair/Dennis Ham, of Dunedin, in their ultra-reliable Peugeot 106.
The SIES moves to Mike Pero Motorsport Park, Ruapuna, in Christchurch on October 4 before the final at Levels Raceway, Timaru on October 18, where the overall three-hour series champion will be awarded the South Canterbury Toyota Cup and New Zealand Endurance Championship title.
