Ngatoa pulled a moved on Lap 5 as he dived down the inside of Auckland's Peter Vodanovich to move up to fourth.
The drivers touched on the exit of the corner and Vodanovich slide across the wet grass into the barriers, having to retire from the race.
Auckland's Callum Hedge had a great fight through the field to come from 10th to pass Ngatoa to finish fourth, with Adams holding off Baldwin and Ransley.
There was further bad news for Ngatoa, as he was penalised for the contact with Vodanovich and dropped back in points to a 15th place finish.
In Race 2 on Sunday morning, Ngatoa finished seventh, with Adam winning the race ahead of Baldwin and Hedge.
For the final race that afternoon, Ngatoa finished well back in 12th place, with Hedge getting the checkered flag in a swap with Adam, while Ransley improved from fourth in the second race to third.
Adam therefore left Pukekohe with a handy points lead over Hedge, followed by Baldwin and Ransley.
Ngatoa, now 125 points back from the leader, will have a bit of work to do when the second round of the championships is held at Pukekohe, this time with a short track configuration, on December 7-9.
Toyota 86 Championship 2018-2019 Driver Standings
1. Connor Adam 217; 2. Callum Hedge 189; 3. Jordan Baldwin 188; 4. Jaden Ransley 174; 5. Jake Klein 143; 6. Brock Gilchrist 130; 7. Andrew Jackson 111; 8. Justin Allen 101; 9. Campbell Stewart 95; 10. Kaleb Ngatoa 92; 11. Sam Wright 90; 12. Arran Crighton 85; 13. Mitch Hughes 84; 14. Jacob Cranston 84; 15. Peter Vodanovich 81; 16. Connor Davison 66; 17. Tony Austin 56.