Although Castroneves came across the finish line first, he forfeited the win after being penalized for blocking Penske Racing teammate Will Power following the final restart with four laps to go.
Dixon zoomed past Power to take second just before they crossed the finish line and Indy Racing League official Brian Barnhart immediately charged Castroneves with blocking and issued him a drive-through penalty.
Following the race, Castroneves, who ended up in 10th place, scuffled with IRL officials.
Points leader Power was awarded second and Dixon's Target Chip Ganassi Racing teammate Dario Franchitti claimed third place.
Ryan Briscoe was fourth and Ryan Hunter-Reay completed the Top 5.
Ganassi's Jamie McMurray won the Brickyard 400 NASCAR race earlier Sunday.