While appearing on "Good Morning America" on Thursday, Ennis said the team attempted to intervene by telling police she was the same woman who previously recanted allegations against the linebacker.
"Even when I called the police, the 49ers came up there (to the hotel) ... I have pictures of the 49ers coming up there trying to talk to the police, telling them I'm the same ex-girlfriend that set up there and lied," Ennis said.
Later Thursday, the team denied any wrongdoing.
"The 49ers fully cooperated with authorities, assisted in locating Mr. Foster, and in no way impeded their investigation," the team said in a statement obtained by Eric Branch of the San Francisco Chronicle.
Foster was released shortly after his arrest. The Washington Redskins claimed him two days later and said they held their own investigation into the domestic violence claims. For now, the former first-round pick remains on the commissioner's exempt list and is ineligible to play.