The lawsuit was filed in Lee County, Fla., state court on Tuesday.
The woman's attorneys said the woman became pregnant as a result of the alleged attack but had a miscarriage.
"I had thought I was going to play tennis with a man who up to that point had been nothing but friendly to me and my kids," said the woman, who identifies herself as a 35-year-old single mother of two, in a statement. "After 10 months of emotional turmoil from the assault, losing the baby and watching him go unprosecuted, I have realized this difficult step is the only way Mr. Santana will be held accountable."
The state attorney's office didn't pursue criminal charges as it never received a complaint.
Santana acknowledged the lawsuit following the Mets' 1-0 victory over the Colorado Rockies on Tuesday.
"No, I mean everything is still the same," Santana told ESPNNewYork.com. "My only comment is that [it's] a legal matter. The truth will come out so I'm just going to wait and see but I can't give any further comments at this time."
Mets manager Jerry Manuel declined comment on the suit when asked by ESPNNewYork.com before Wednesday's game.
John Clune, who is co-counsel for the accuser, told ESPN's Shelley Smith the accuser is filing the suit now because it took three months for police investigators to decide not to pursue the criminal case.
"In January, when she found out they would not file the case, we went into negotiations with the defense," Clune said. "In the end, she filed because she thought Santana wasn't taking it serious enough."
Clune, a Denver-based attorney whose firm specializes in representing crime victims, also represented the family of the accuser in the Kobe Bryant case.
Asked why the prosecution didn't file charges in this case, he said: "In my opinion, rape cases are hard cases to prove and celebrity rape cases are highly scrutinized. A lot of regular sex assault cases never get filed."
Santana told Florida police he had consensual sex with the woman on a golf course in a gated Lee County community on the night of Oct. 27, 2009.
A case report from the Lee County Sheriff's Office dated Jan. 12 said Santana told investigators that the woman "never told me to stop or 'No' during our sexual encounter."
The woman told detectives Santana forced himself sexually on her, though she repeatedly told him she didn't want to have sex. Afterward, she said she watched him play tennis.
According to the police report, on the day after the alleged incident, the accuser underwent a medical examination, which showed no injuries to the vaginal area and a negative result for the presence of semen.
Kathy Redmond, the founder of the National Coalition Against Violent Athletes, told ESPN's Smith that the accuser contacted her directly after the incident. Despite the police report, Redmond claimed that some DNA evidence was present.
"The prosecution said her statement didn't correspond with what other witnesses said," Redmond said. "There were no other witnesses except for his entourage back at the tennis court."
The accuser suffers from multiple sclerosis, which results in some balance issues, but she is able to play tennis and go for long walks, according to Redmond. Clune confirmed to the New York Daily News that she suffers from the condition.
Information from ESPNNewYork.com's Ian Begley, ESPN's Shelley Smith and The Associated Press was used in this report.