Le clinched the New Zealand Grand Prix curtain raiser, converting pole position to a win in the top eight reverse grid.
Wharton, who started third, beat New Zealand’s Liam Sceats into the bus stop chicane and never ceded second place.
Ryan Wood wound up finishing sixth after side-to-side contact with MTEC Motorsport teammate Louis Sharp through the chicane speared the Supercars star off the road and across the grass.
Great Britain’s Freddie Slater, who is a serious threat for the title, finished fifth while title rival Ugo Ugochukwu was seventh.
The race featured three incidents. Trevor Latourrette spun at the Turn 3 and 4 esses.
China’s Yuanpu Cui brought out the first Safety Car on Lap 9 when he went off at the Turn 9 hairpin from 12thl.
Racing resumed on Lap 14 but it wasn’t long before the Safety Car returned and brought an early end to the contest.
Brazil’s Ricardo Baptista parked his car backwards in the gravel trap at Turn 11 after the bridge.
“First off I want to say thank you to Hitech,” said Le, whose win came at the same circuit where Tsunoda last won in 2020.
“It’s been a difficult weekend and last weekend, but I’m very happy to be able to get the win and am very grateful for this.
“James was keeping me on the edge of my seat and I had to be focused on every single lap. It was quite difficult. Not an easy win.”
Wharton said he didn’t have enough to beat Le, but wasn’t unhappy to finish second.
“It was a good race but Kanato is a person you don’t mind coming second to,” said Wharton.
“He works hard and he’s one of the nicest guys here. Second is not too bad.
“We don’t quite have the pace of the faster cars, but we maximised our race then.”
The Formula Regional Oceania Trophy comes to a close with the 70th running of the New Zealand Grand Prix at 2:33pm AEDT.
With one race remaining, Ugo Ugochukwu leads Freddie Slater by 25 points. A maximum 35 points are available for the New Zealand Grand Prix, in which Slater will start fourth while Ugochukwu starts last due to a penalty.
Results: Formula Regional Oceania Trophy Highlands, Race 2
| Pos | Num | Driver | Laps/Diff |
| 1 | 19 | Kanato Le | 18 laps |
| 2 | 13 | James Wharton | 0.421 |
| 3 | 23 | Liam Sceats | 1.140 |
| 4 | 11 | Louis Sharp | 1.663 |
| 5 | 27 | Freddie Slater | 2.042 |
| 6 | 40 | Ryan Wood | 2.967 |
| 7 | 4 | Ugo Ugochukwu | 3.304 |
| 8 | 12 | Jin Nakamura | 4.128 |
| 9 | 21 | Yevan David | 4.443 |
| 10 | 3 | Zack Scoular | 4.712 |
| 11 | 52 | Nolan Allaer | 5.013 |
| 12 | 50 | Jack Taylor | 5.376 |
| 13 | 33 | Fionn McLaughlin | 5.596 |
| 14 | 14 | Cooper Shipman | 5.935 |
| 15 | 41 | Ricardo Baptista | 3 laps |
| 16 | 22 | Sebastian Manson | 5 laps |
| DNF | 8 | Trevor LaTourrette | Lap 10 |
| DNF | 5 | Yuanpu Cui | Lap 8 |
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