Owned by Jerry and Ann Moss, Zenyatta received 10 of 19 first-place votes with Rachel Alexandra getting the remaining nine votes. Zenyatta, trained by John Shirreffs, garnered a total of 181 points to 'Rachel's 176.
"She could run again today," said Shirreffs on Sunday morning.
Jockey Mike Smith guided the five-year-old mare through her undefeated 2009 season of five starts and $3.3 million. Zenyatta is perfect in all 14 career starts for $5,474,580.
Zenyatta became the first horse to win two different Breeders' Cup races and the first female to capture the Classic. Last year she won the Breeders' Cup Ladies' Classic.
No announcement has been made, but Zenyatta is expected to be retired from racing.
Rachel Alexandra received a total of 176 points in the final poll after leading the voting for more than two months. The three-year-old filly is currently resting for an expected 2010 campaign.
Classic runner-up Gio Ponti finished third with 140 points. The four-year-old colt won the Arlington Million this year and finished 2009 with four wins in seven starts for $2,333,000.
"He had a very nice career this year. He won four Grade Ones and finished second in two other Grade Ones," trainer Christophe Clement said. "He should look very good for (the Eclipse Award as champion turf horse) and champion older horse, maybe. But I'm just the trainer. I don't vote."
Belmont Stakes and Travers winner Summer Bird was fourth in the Classic and finishes fourth in the poll, collecting 100 points. Summer Bird has been invited to compete in the Japan Cup Dirt overseas.
Two-time Breeders' Cup Mile winner Goldikova received 94 points to finish in fifth-place. It was the second straight year the filly triumphed over male horses in the turf event.
Finishing in sixth-place was Conduit, repeat winner of the Breeders' Cup Turf. The four-year-old colt acquired 80 points in the balloting. Conduit will have one more start this year for trainer Sir Michael Stoute to close out his career in the Japan Cup later this month before going to stud next year in Japan.
Informed Decision, winner of the Breeders' Cup Filly & Mare Sprint, got the seventh spot with 65 points. Trained by Hall of Famer Jonathan Sheppard, Informed Decision will race again next year and continue in sprints.
John Shirreffs also trains the eighth-place horse, Life Is Sweet. The four- year-old filly received 65 points following her win in the Ladies' Classic.
"Life Is Sweet is such a talented filly in her own right," said Shirreffs.
Owner-breeders Marty and Pam Wygod will decide whether the four-year-old filly is kept in training for another year or joins Zenyatta as a broodmare.
Moving up one spot to ninth in the poll is Presious Passion, second in the Breeders' Cup Turf. Trained by Mary Hartmann, the six-year-old gelding received 50 points.
"The owners have talked about a race in Hong Kong later this year," said Hartmann, "but we'll evaluate him when he gets home (New Jersey) and make a decision then. We'll definitely be taking him to Gulfstream Park again this winter."
Rounding out the top 10 is Breeders' Cup Juvenile runner-up Lookin At Lucky. The two-year-old colt, trained by Hall of Fame member Bob Baffert, got 11 points.