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Stoner, starting from pole after destroying the track record in Saturday qualifying, briefly surrendered the lead to Honda team mate Dani Pedrosa but roared past the Spaniard seven laps later and then powered his way to a runaway victory.
Pedrosa, last year's winner at the Brickyard, settled for second, crossing nearly five seconds back, while American Ben Spies gave the home crowd something to cheer, taking third.
With a 10th consecutive podium finish, Stoner extended his lead at the top of the standings over Spain's world champion Jorge Lorenzo, who finished fourth, to 44 points with six races to run.
DOMINATING DISPLAY
"There are crucial points throughout the whole season and we just have to make sure we keep our heads down and keep trying to win races," Stoner told reporters. "That's what I enjoy most and it's what we are here to do every weekend."
It was another dominating display by Stoner, who had complained bitterly all week about the slippery track he labeled one of the worst on the MotoGP circuit.
But there was no hint of distress in the Australian's performance as he neatly navigated the 4.22-km layout, which uses part of the Indianapolis Motor Speedway's oval on another sweltering day at the famed Brickyard.
"I'm not like some other riders who just enjoy tracks because they win there," said Stoner, the 2007 world champion. "I've won on most of the circuits we have on the calendar and I can't honestly say this is better than most of them.
"We ride on some fantastic circuits; I don't get a kick out of it just because I win.
"I was struggling a little bit with the grip and didn't feel comfortable but I suppose, compared to everyone else, we felt pretty good."
NO HOPE
Both Pedrosa and Spies agreed they had no hope of reeling in Stoner.
Pedrosa started behind Stoner on the second row but shot into the lead on the first turn.
Some early wobbles dropped Stoner down to third but the Australian stalked the leaders and before the race reached the midway point was in complete command.
"I knew for the race pace I was not there," said Pedrosa. "I did a couple of good first laps but then Casey went by and started to pull away. I kept focused on my rhythm and I was happy with my performance."
One rider not pleased with his day's work was seven-times world champion Valentino Rossi, who had a miserable weekend with a 10th place finish.
After crashing in qualifying, the Italian started well down the grid and laboured to his worst result of the season.
Results from the 2011 Indianapolis MotoGP
1 Casey Stoner (AUS) Honda 46min52.786
2 Dani Pedrosa (ESP) Honda +4.828
3 Ben Spies (USA) Yamaha +10.603
4 Jorge Lorenzo (ESP) Yamaha +16.576
5 Andrea Dovizioso (ITA) Honda +17.202
6 Alvaro Bautista (ESP) Suzuki +30.447
7 Colin Edwards (USA) Yamaha +39.690
8 Randy de Puniet (FRA) Ducati +53.416
9 Hiroshi Aoyama (JPN) Honda +53.790
10 Valentino Rossi (ITA) Ducati +55.345
Overall standings after 11 races
1 Casey Stoner (AUS) Honda 243
2 Jorge Lorenzo (ESP) Yamaha 19
3 Andrea Dovizioso (ITA) Honda 174
4 Dani Pedrosa (ESP) Honda 130
5 Ben Spies (USA) Yamaha 125
6 Valentino Rossi (ITA) Ducati 124
7 Nicky Hayden (USA) Ducati 105
8 Colin Edwards (USA) Yamaha 84
9 Marco Simoncelli (ITA) Honda 80
10 Hiroshi Aoyama (JPN) Honda 77
Moto2
1 Marc Marquez (ESP) Suter 45min 50.601
2 Pol Espargaro (ESP) FTR +1.889sec
3 Esteve Rabat (ESP) FTR +2.310
4 Bradley Smith (GBR) Tech3 +3.389
5 Scott Redding (GBR) Suter +5.674
Overall standings (after 11 races)
1 Stefan Bradl (GER) Kalex 193
2 Marc Marquez (ESP) Suter 165
3 Andrea Iannone (ITA) Suter 96
4 Alex DeAngelis (RSM) Motobi 96
5 Simone Corsi (ITA) FTR 93
125 cc
1 Nicolas Terol (ESP) Aprilia 42min11.978
2 Maverick Vinales (ESP) Aprilia +3.633
3 Sandro Cortese (GER) Aprilia +3.737
4 Sergio Gadea (ESP) Aprilia +4.227
5 Johann Zarco (FRA) Derbi +14.186
Overall standings (after 11 races)
1 Nicolas Terol (ESP) Aprilia 191
2 Johann Zarco (FRA) Derbi 165
3 Maverick Vinales (ESP) Aprilia 152
4 Sandro Cortese (GER) Aprilia 147
5 Jonas Folger (GER) Aprilia 117
