Pole sitter Sergio Gadea initially held his advantage at the head of the field during the opening laps of the 'first' race, while Bradley Smith plummeted backwards from second on the grid to the lower end of the top 20.
The Polaris World Aprilia rider then repeatedly set fastest race laps and was up to ninth place - just ahead of Gadea, who seemed to suffer most when the first drops of rain began to fall - by lap 14 of 24, when increasing rain forced the race to be stopped.
With not enough laps complete to call it a result, a second five lap race - starting in the order present when the race was stopped - was used to decide the 2008 French 125GP.
The grid thus assembled for the shootout, on full wet tyres and with rain still falling, with Joan Olive on pole ahead of Nicolas Terol, Stefan Bradl, Gabor Talmacsi, di Meglio, Simone Corsi, Esteve Rabat, Pol Espargaro, Smith and Gadea.
Olive fumbled his getaway, while Rabat grabbed the advantage into turn one - then promptly span out on the exit of the turn. World champion Talmacsi suffered a similar fate, highsiding out of the lead at the end of lap two, handing the advantage to Smith.
But by now the vocal French fans were on their feet for di Meglio, up to second and looking for a place to pass. The Ajo Derbi rider made his victory move later in the lap, then soaked up pressure from Smith to stay 0.8secs clear at the chequered flag.
Terol completed the podium, but world championship leader Corsi could only manage 13th position and has now slipped to third in the standings - twelve points behind new leader di Meglio and four points from Terol.
Race results - Le Mans:
1. di Meglio (Derbi)
2. Smith (Aprilia) +0.800secs
3. Terol (Aprilia) +3.077secs
4. Espargaro (Derbi) +10.407secs
5. Iannone (Aprilia) +11.697secs
6. Bradl (Aprilia) +11.881secs
7. Zanetti (Aprilia) +16.372secs
8. Olive (Derbi) +16.545secs
9. de Rosa (KTM) +19.163secs
10. Krummenacher (KTM) +22.391secs
21. Webb (Aprilia) +34.810secs
Redding (Aprilia) DNF