The McLaren driver, seven points behind Schumacher with just the Japanese Grand Prix to come, seized what could prove to be a crucial advantage in the closest title battle in years as Schumacher managed only the seventh best time.
Colombian Juan Pablo Montoya, three points behind the German, was fourth fastest for Williams.
Finland's Raikkonen will share the front row with Schumacher's Brazilian teammate Rubens Barrichello, winner last year in a controversial finish when Schumacher slowed at the line after leading until then.
Montoya starts next to Frenchman Olivier Panis in a Toyota, his best qualifying of the season.
Montoya's teammate Ralf Schumacher, younger brother of Ferrari's defending champion, will be on the third row with Spaniard Fernando Alonso of Renault.
Michael Schumacher shares the fourth row with Briton David Coulthard, Raikkonen's teammate.
Montoya's fans, packing the main grandstand with banners and flags, roared in delight when Schumacher's time flashed up, slower than both Raikkonen and Panis.
They soon had more to celebrate when Alonso, winner for Renault in Hungary, went out next and pushed the German further down the grid.
Sunday's race at Indianapolis will be the first time Schumacher has not started on pole at the circuit, which first hosted a Grand Prix in 2000.
USA qualifying results
Posn
Driver
Timing
1
Kimi Raikkonen
1:11.650
2
Rubens Barrichello
+ 0.144
3
Olivier Panis
+ 0.270
4
Juan Pablo Montoya
+ 0.298
5
Ralf Schumacher
+ 0.428
6
Fernando Alonso
+ 0.437
7
Michael Schumacher
+ 0.544
8
David Coulthard
+ 0.647
9
Cristiano da Matta
+ 0.676
10
Jarno Trulli
+ 0.916
11
Jenson Button
+ 1.045
12
Jacques Villeneuve
+ 1.400
13
Nick Heidfeld
+ 1.433
14
Mark Webber
+ 1.619
15
Heinz-Harald Frentzen
+ 1.797
16
Justin Wilson
+ 1.935
17
Giancarlo Fisichella
+ 2.148
18
Ralph Firman
+ 2.377
19
Jos Verstappen
+ 3.710
20
Nicolas Kiesa
+ 3.994
