Bailey won the third race, a mile-and-an-eighth allowance, on Ground Storm, for his 49th victory to break the meet record he set here in 1997.
Bailey, who set a world record of 9.84 seconds in the Atlanta Games, won the 100 comfortably in 10.17.
Bailey defended Sheppard and won an acquittal in the second trial.
He can become the first rider not named Bailey to win the Saratoga riding title since 1998.
But Bailey pulled away in the final 10 meters and won in 10.03 seconds.
Bailey won $1.5 million for winning the race in which Johnson pulled up around the 110 m mark with an injured quadriceps muscle.
Bailey won the race, completing it in a time of 15 seconds and winning the 1.5 million dollar prize.
Still, Bailey has ridden in 620 races this year and won 161, a 26 percent success rate.
Bailey won the race and the $1.5 million prize that came with the victory, Johnson received $500,000.
Bailey ran and won the Democratic primary with a plurality of 23% in an 11 candidate field.