The Hal Wiggins trainee, under jockey Calvin Borel, covered the 1 1/16-mile distance in a stakes-record time of 1:43.08. The previous record was 1:43.82 set in 2001 by Belterra.
The winner was 4 3/4 lengths in front of second-place finisher Sara Louise, who was another 7 1/4 lengths in front of third-place War Echo.
Rachel Alexandra returned $8.20, $4, and $2.80. Sara Louise paid $3 and $2.40, while War Echo returned $3.40. The exacta paid $20.20 and the trifecta returned $77.20.
A daughter of Medaglia d' Oro, Rachel Alexandra broke first and stayed near the rail as she led the field through fractions of :23.75 for the first quarter of a mile, with the half mile going in :47.85. Three quarters went in 1:12.55.
War Echo, who tried to overtake the winner down the backstretch, was content to remain in second in the early going, while Super Poni held third until she was overtaken by Sara Louise as the field neared the turn for home. Sara Louise tried to run down Rachel Alexandra as the field came down the straight, but the winner dug deep and pulled away.
Prior to the Golden Rod, Rachel Alexandra finished second, beaten 3 3/4 lengths by Sara Louise, in the Pocahontas Stakes (gr. III) Nov. 1 under the Twin Spires.
Rachel Alexandra improved her career record to 3-2-0 from six starts and increased her earnings to $201,440.
Bred in Kentucky by her owner, Dolphus Morrison, who races the filly in partnership with Michael Lauffer, Rachel Alexandra was produced from the Roar mare Lotta Kim, who finished second in the Golden Rod in 2003.
Plans call for Rachel Alexandra to receive some time off before going to either Oaklawn Park or Fair Grounds to prep for the Kentucky Oaks (gr. I).