Most of the field chose intermediate tyres for the wet but drying conditions, under which Lotus Aprilia's pole sitter Debon emerged into an early lead from KTM's Hiroshi Aoyama.
But Debon had gone for a 'dryer' set-up, and initially came under pressure from Aoyama on the wetter sections of the track, but the Spaniard resisted the challenge and began to disappear into the distance as the track conditions began to play ever more into his hands.
The experienced #6, brought in to replace Jorge Lorenzo after the double world champion's move to MotoGP, was ten seconds clear at one stage, but eventually backed off to a safe five second victory margin.
The fight for second was a much closer contest, with star rookie Mattia Pasini's slick tyres paying dividends towards the end of the race, when he snatched the runner-up spot from Yuki Takahashi.
But Marco Simoncelli was also on the attack - and snatched second from the Polaris world Aprilia rider at the very final turn. Takahashi took fourth, while Aoyama faded backwards to seventh on a day when team-mate and world championship leader Mika Kallio crossed the line in fifth.
Kallio now leads Pasini by 16 points, with Debon 18 points further back in third.
Race results - Le Mans:
1. Debon (Aprilia)
2. Simoncelli (Gilera) +4.816secs
3. Pasini (Aprilia) +4.998secs
4. Takahashi (Honda) +5.770secs
5. Kallio (KTM) +6.197secs
6. Poggiali (Gilera) +6.474secs
7. Aoyama (KTM) +14.909secs
8. Simon (KTM) +17.526secs
9. Espargaro (Aprilia) +32.925secs
10. Faubel (Aprilia) +36.719secs
Laverty (Aprilia) DNF