Kentucky native Nicky Hayden will start sixth, and California rider Colin Edwards qualified in the 12th position.
American Ben Spies crashed during the morning practice session, injuring his left shoulder. The injury will prevent Spies from racing this weekend.
Scott Redding will start from position one for the 25-lap Moto2 race. He will be joined on the front row by Pol Espargaro and Takaaki Nakagami.
Espargaro won the former 125cc class race at IMS in 2009 and captured the pole position in 2012.
The three riders starting up front for the Moto3 race are also the riders that have recorded victories in four of the the first eight races of the season.
Alex Rins grabbed the pole position followed by Alex Marquez and Maverick Vinales. All three are riding Austrian manufactured KTM motorcycles.
Rins has won twice in 2013 and is coming off a win, Vinales also has two wins on the year. Four-time winner Luis Salom will start 10th in the 23-lap race.