The 27-year-old Briton added to the title he claimed in 2004 and also gave the Ten Kate Honda team their first championship after five years of trying.
Noriyuki Haga won the race in dominant fashion for Motor Italia Yamaha and agonisingly missed out on the title by just two points, having started the day 29 behind Toseland.
As he did in race one it was Haga, who began the race 17 points behind Toseland in the title race, who burst through to the front on his Motor Italia Yamaha, with his team-mate Troy Corser covering his rear for the opening handful of laps.
Haga was untroubled at the front and duly converted his lead into his sixth victory of the season and the 26th of his career by over four seconds.
"It was a little bit easy because we changed the suspension setting for the race and went with a tyre a little bit harder than before," Haga said.
"I don't have any complaints. I won twice today, I did all I could, but it was not enough. I'll just try again next year for the championship title."
Corser was nothing like as safe in second and lost the position to Max Biaggi's Alstare Suzuki on lap 11. Try as he might though, the veteran Italian could so nothing about Haga.
Corser began to suffer problems with his rear tyre and was soon being pressured by the PSG-1 Kawasaki of Fonsi Nieto.
Twice the Spaniard passed him at the Adelaide hairpin and twice Corser grabbed the place back immediately under acceleration. Mindful of this, Nieto pulled a dangerous move on his rival on lap 20, shoving Corser fairing to fairing, giving him the option to back off or be taken off.
He backed off and settled for fourth behind Nieto, who gave his team their best result since Assen last year, on what was his last appearance for them too.
An off-form Troy Bayliss sat behind Toseland in seventh place during the early stages, with both trying to avoid the wayward riding of Suzuki Germany's Max Neukirchner.
The German got by them both, with Toseland narrowly avoiding a collision on lap seven, but his race ended on a flat note as he crashed out on lap 11.
Toseland was passed by Bayliss' Ducati, but still came home sixth, which was just enough to make him Britain's first two-time champion since Carl Fogarty in 1995.
Following him home was his team-mate Roberto Rolfo, who passed Regis Laconi's Kawasaki, Michel Fabrizio's DFX Honda and Ruben Xaus' Sterilgada Ducati in the last four laps.
Local riders Yoann Tiberio and Guillaume Dietrich both took the best finishes of their careers in 12th and 13th for Alto Evoluion Honda and Alstare Suzuki while Britain's Dean Ellison finished the season with a point for 15th on his Pedercini Ducati.
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