The race was a flag-to-flag thriller as Miller braved mixed conditions, a trip into the gravel and two long-lap penalties for speeding in the pitlane.
Hopes were high after the Australian qualified on the front row in P3 and took the lead at the start of the race.
It did not take long for the rain to bucket down at Le Mans and riders had to come into pit lane to change to their wet-weather bikes.
With that came the scary moment Miller ran off the track and into the gravel.
Luckily, he managed to regain control and make his way back onto the track.
After being caught speeding in the pitlane, the Aussie had to serve two-long lap penalties.
The Aussie’s pace was so strong in the wet conditions, that he served those penalties and still passed Fabio Quartararo for the race lead and the eventual victory on a drying track.
The factory Ducati rider was joined on the podium with Johann Zarco (Pramac Ducati) and Quartararo (Yamaha) in third.
Miller shared after the race; "Hectic, very hectic, I mean, it was perfectly still just before but halfway through the race when the rain came, the wind came with it and it was…. honestly, as I came down pitlane, the barrier blew into pitlane and I said they are going to red flag this for sure, but then it dropped off relatively quickly.
“The first couple laps were dodgy on the wet tyres, but I got going and then I had the long laps, I wasn’t sure why, apparently for speeding. I generally do get speeding tickets in France, not the ones I want!
“I was able to bosh them out pretty quickly and get to work on Fabio and I got in front of him, and I just felt comfortable to be honest, I was just riding into the conditions, I saw Johann was coming so I had to up her a bit for the last five laps, but the track was pretty much dry again.
“I was thinking do I pit or not, because it such a long pit road here and you lose a lot of time so I was just counting down the laps but, yeah, absolutely amazing I can’t believe it.
“Back-to-back wins is just fantastic, and I can’t thank the team enough, they’re awesome.”
Miller’s victories have put him right back into the championship hunt with the Aussie now only trailing series leader Quartararo by 16 points.
The Aussie returns to the track for Ducati’s home race at Mugello on 28-30 May.