McLaren and Ferrari began Part Two of their fierce battle with Hamilton taking the top spot early. However, his team-mate, Fernando Alonso took top spot midway through. Felipe Massa, Kimi Räikkönen, and Heidfeld along with the two McLarens made the Top 5 again. Webber made it to the next session, although his team-mate Coulthard was relegated along with 2002 United States Grand Prix Champion Rubens Barrichello. Barrichello's partner Jenson Button was also relegated, along with Nico Rosberg, Anthony Davidson, and Ralf Schumacher.
In Part Three, Räikkönen, Alonso, Hamilton, Massa, and Heidfeld all had their eye on Pole Position. Hamilton was first out and had the quickest time with a 1:13:089. Alonso was about four tenths behind, followed by Heidfeld and the Ferraris. Giancarlo Fisichella and Heikki Kovalainen, both Renault drivers, also were near the top, but Jarno Trulli and Webber knocked Fisichella down. With about 5 minutes left, Massa took first spot and Räikkönen took second. Hamilton was bumped to third, Alonso fourth, and Heidfeld remained fifth. About one minute later, Hamilton took the top spot, and Alonso second. Alonso had one lap left, but could only get within about 2 tenths of a second of rookie teammate Lewis Hamilton. Massa and Räikkönen were dropped to third and fourth respectively. Heidfeld held on to fifth, with Kovalainen in sixth, bouncing back from his disappointing 22nd starting position in Canada. Vettel finished seventh, just two spots behind his temporary partner, Heidfeld. Trulli was 8th, with Red Bull-Renault's Mark Webber ninth and Fisichella tenth.
Lewis Hamilton, on the pole, sped off the grid. Fernando Alonso stayed close behind, followed by the Ferraris. The drama in turn 1 was in the middle of the pack. Vettel ran wide and lost places, but escaped damage. Ralf Schumacher, who started in 12th, turned in late, and ended up crashing into David Coulthard, who he had started alongside. Jenson Button and Nico Rosberg, 13th and 14th respectively, escaped but Rubens Barrichello got caught up. Ralf was out on the spot, while Coulthard and Barrichello limped back to the pits and retired.
Also, Kimi Räikkönen was caught by Nick Heidfeld and Heikki Kovalainen. Räikkönen would soon get his revenge. Up front, the top four were running strongly until the pit stops came around. The top 4 all went in early, soon followed by Heidfeld in the BMW Sauber, leaving sixth place qualifier Kovalainen in first. He lead six or seven laps, and Hamilton then regained the lead.
Despite a mid-race challenge from team-mate Fernando Alonso, in which the two McLaren drivers were racing side-by-side for the lead down the main straight, Hamilton maintained the lead to win his second-ever Formula 1 Grand Prix race, the other victory being in the previous event at Montreal. This marked the first win for a black driver, McLaren's first 1-2 finish at the circuit, and their first win at Indianapolis since Mika Häkkinen's final Grand Prix win in 2001.
Takuma Sato spun off at turn 3 after managing to pass Spyker's Adrian Sutil. Sato had been due a drive-through penalty for overtaking under yellow flags, but this was changed to a 10-place grid penalty for the next race.
There were also three mechanical retirements - Nico Rosberg in the Williams suffered an engine failure with only five laps to go, while BMW Sauber's Nick Heidfeld and Toro Rosso's Vitantonio Liuzzi also retired from the race due to mechanical failure.
| Pos | Name | Constructor | Part 1 | Part 2 | Part 3 |
|---|---|---|---|---|---|
| 1 | Lewis Hamilton | McLaren-Mercedes | 1:12.563 | 1:12.065 | 1:12.331 |
| 2 | Fernando Alonso | McLaren-Mercedes | 1:12.416 | 1:11.926 | 1:12.500 |
| 3 | Felipe Massa | Ferrari | 1:12.731 | 1:12.180 | 1:12.703 |
| 4 | Kimi Räikkönen | Ferrari | 1:12.732 | 1:12.111 | 1:12.839 |
| 5 | Nick Heidfeld | BMW Sauber | 1:12.543 | 1:12.188 | 1:12.847 |
| 6 | Heikki Kovalainen | Renault | 1:12.998 | 1:12.599 | 1:13.308 |
| 7 | Sebastian Vettel | BMW Sauber | 1:12.711 | 1:12.644 | 1:13.513 |
| 8 | Jarno Trulli | Toyota | 1:13.186 | 1:12.828 | 1:13.789 |
| 9 | Mark Webber | Red Bull-Renault | 1:13.425 | 1:12.788 | 1:13.871 |
| 10 | Giancarlo Fisichella | Renault | 1:13.168 | 1:12.603 | 1:13.953 |
| 11 | David Coulthard | Red Bull-Renault | 1:13.424 | 1:12.873 | |
| 12 | Ralf Schumacher | Toyota | 1:12.851 | 1:12.920 | |
| 13 | Jenson Button | Honda | 1:13.306 | 1:12.998 | |
| 14 | Nico Rosberg | Williams-Toyota | 1:13.128 | 1:13.060 | |
| 15 | Rubens Barrichello | Honda | 1:13.203 | 1:13.201 | |
| 16 | Anthony Davidson | Super Aguri-Honda | 1:13.164 | 1:13.259 | |
| 17 | Alexander Wurz | Williams-Toyota | 1:13.441 | ||
| 18 | Takuma Sato | Super Aguri-Honda | 1:13.477 | ||
| 19 | Vitantonio Liuzzi | Toro Rosso-Ferrari | 1:13.484 | ||
| 20 | Scott Speed | Toro Rosso-Ferrari | 1:13.712 | ||
| 21 | Adrian Sutil | Spyker-Ferrari | 1:14.122 | ||
| 22 | Christijan Albers | Spyker-Ferrari | 1:14.597 | ||