The Target Chip Ganassi driver posted the best lap of 1 minute, 38.3918 seconds on Saturday to edge Team Penske driver Will Power of Australia by 0.0276 seconds. American driver Graham Rahal was third. Toronto's James Hinchcliffe will start fifth and Alex Tagliani of Lachenaie, Que., finished 15th overall.
"We gradually worked on the car and made it better and better," said Dixon, who won here in 2009. "It took us a bit of time but we finally got it right."
Ryan Briscoe of Australia was fourth followed by Canadian rookie James Hinchcliffe in fifth and defending champion Helio Castroneves in sixth.
Danica Patrick, who had her only IndyCar win here in 2008, will start 23rd in her final IndyCar series road event. The final two races of the season in Kentucky and Las Vegas are on ovals. Patrick will make a full-time move to NASCAR next season.
"We had some problems with the gearbox today," Patrick said. "The car wasn't downshifting or upshifting properly. The last lap was the same as the two laps before and I know I lost time shifting the car."
The deadly March 11 earthquake damaged the 1.5-mile oval at Twin Ring, so Sunday's race will be held instead on the recently repaved 14-turn road course.
Power is currently in second place in the IndyCar Series standings with 502 points, just five behind leader Dario Franchitti.
Franchitti will start a season-low ninth on a road course.
"Dario starting ninth is good for us, although a lot can happen in a race," said Power, who will make his ninth front-row start of the season. "We always try to put ourselves in the position to stay out of trouble and give us the best chance of winning."
The qualifying divided the field into two groups of 13 drivers to compete in 15-minute timed rounds. The top six drivers in each group moved on to the pool of 12 drivers for round two, a 10-minute timed round. Finally, the top six drivers from round two competed for placement for positions one through six for Sunday's race in a 10-minute timed round.
Sunday's race will be the last IndyCar series event in Japan. Mobilityland Corp., a wholly owned unit of Honda Motor Co., announced in February that due to the economic downturn the 2011 race will be its last IndyCar race at the Twin Ring Motegi circuit.