Sixth place went to a hard charging Alex de Angelis, but the San Marinese may find the position taken from him pending the results of a post-race investigation. The San Carlo Honda Gresini rider tangled with injured Repsol Honda Dani Pedrosa while passing the Spaniard for seventh at half-race distance.
Pedrosa, who had just been overtaken by Chris Vermeulen, drifted slightly off line on the exit of a left hander - prompting de Angelis to dive for the inside. Unfortunately, their lines crossed and Alex hit the side of Pedrosa's RCV with considerable force, although the Spaniard stayed in control despite his feet coming off the pegs.
Pedrosa, riding at '60-70 percent' fitness following recent knee and forearm surgery, seemed shaken by the incident - which may well have aggravated his injuries - and, having fought his way up from 14th on the grid to sixth, sank back to eleventh at the finish.
Pedrosa only just held off former team-mate Nicky Hayden, himself riding battered, bruised and with three stitches in his chest after a huge qualifying fall. The American had begun his 100th grand prix, and first race for Ducati Marlboro, from 16th on the grid.
Vermeulen brought the sole surviving Suzuki home in a less-then-expected seventh position, and had impressive MotoGP rookie Mika Kallio breathing down his neck, while Honda riders Toni Elias and Randy de Puniet completed the top ten.
Behind Hayden, Sete Gibernau's first MotoGP since 2006 saw the injured Spaniard progress just one place from 15th on the grid for Grupo Francisco Hernando.
Fellow former title runner-up Marco Melandri looked set to give the Hayate Racing Team a thrilling debut as he concluded the first lap in eighth position, but the Italian - who turned heads with fifth in Saturday free practice, before qualifying the 'unofficial' Kawasaki ZX-RR eleventh - then ran straight on through the turn one gravel.
Melandri rejoined last, but pushed hard to the flag and was able to finish ahead of Yuki Takahashi, James Toseland (who also ran off track) and Niccolo Canepa.
Qatar Grand Prix:
6. de Angelis
10. de Puniet