Soto, 27, was laid to rest Wednesday, and Jeter reached out to her mother, Donna Soto, just hours after the funeral.
The Yankees confirmed Jeter made the phone call.
Soto's sister, Carlee, tweeted about the visit.
Derek Jeter just called my mom!!!!! 💙 Thanks Vicki, she needs it 💚 thank you @yankees this meant a lot to my mother and all of us. ⚾💙— Carlee Soto (@ICarlee23) December 19, 2012
With Wednesday's phone call, Jeter became the latest New York-area athlete to pay his respects to the families of Sandy Hook victims. Earlier this week, New York Giants wide receiver Victor Cruz met with the family of 6-year old victim Jack Pinto, who was laid to rest wearing his replica Cruz jersey.