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The South African started the weekend 106 points clear of Enea Bastianini and 111 ahead of Jorge Navarro, knowing that beating - or even likely finishing with - them would be enough to wrap things up.
Having qualified seventh, Binder was in the thick of what became a four-rider fight for the lead throughout the 20 laps, with Navarro, Bastianini and Fabio Di Giannantonio.
He led on several occasions, including after a bold, fourth-to-first move into the final corner with four laps to go.
Bastianini led at the start of the final lap, as Binder moved up to second at the first corner, but he was shuffled back down to fourth by Di Giannantonio at Turn 9.
However he was soon back into third, then slipstreamed down the back straight and into the lead entering the final corner.
While Binder ran wide and Navarro snuck through to win by just 0.030 seconds, second place was enough for Binder to secure an unassailable 106-point championship lead with only 100 still up for grabs.
The win was Navarro's second of the campaign, while Bastianini was third.
Binder claimed six podium finishes but no race wins across his first four seasons in Moto3, however he has been the dominant force in 2016.
He won the first time at Jerez, from the rear of the grid after his KTM was found to have run an unhomologated ECU in qualifying, and then again at Le Mans, Mugello, Silverstone and Misano.
With the result, Binder becomes just the third motorcycle grand prix world champion from South Africa.
He is the first since Jon Ekerold won the 350cc title in 1980, which followed Kork Ballington winning the 350cc and 250cc titles in both '78 and '79.
The 21-year-old will stay with Ajo Motorsport next year but move up to Moto2, with KTM's new programme in the class.
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