The Garry Rogers Motorsport driver claimed a lights-to-flag win in the 18-lap encounter, finishing ahead of Johnson in his Ford Mustang while Supercars regular Brodie Kostecki drove his Chevrolet Camaro to third on debut.
A massive moment in the context of the series, the incident is set to be investigated post-race.
There was a Safety Car brought out shortly afterwards, when debutant Tom Hayman (Ford Mustang) went off on the outside at Turn 2, which aided in Kelly's charge through the field from 18th to eighth.
When racing resumed on Lap 7, third-generation racer Johnson made his move on Kostecki into second place, holding off the Erebus Motorsport driver to the chequered flag.
Brett Holdsworth (Ford Mustang) and Lochie Dalton (Ford Mustang) rounded out the top five, while Kyle Gurton (Ford Mustang), Ben Grice (Ford Mustang), Kelly, Elliot Barbour (Chevrolet Camaro), and Jackson Rice (Ford Mustang) completed the top 10.
While personally a great result for Herne, it was bittersweet for his Garry Rogers Motorsport team.
“Yeah it's great, shame what happened to Owen [Kelly], we are title combatants but its a shame to see your team car off at Turn 1, but good to get GRM #1 back up front and with Valvoline, Sydney was a but of a shocker but we've come back here this weekend,” Herne said.
Johnson was elated with his best result in the National Trans Am series.
“That was unbelievable, I got pretty lucky there at Turn 1 but once we got through that I was able to keep my pace, that was unreal,” Johnson said.
The Trans Ams return to the track tomorrow for Race 2 at 12:55 local time/AEST.
Race 2 will be streamed live and ad-free on Stan Sport.