The bodies of Madeline Samaan-Fay and 49-year-old Mourad "Moni" Samaan were discovered in his green Toyota 4Runner in a rural area north of the capital.
The FBI had issued a statewide Amber Alert on Friday for the toddler. She was taken by her father after her mother was granted custody, ending what had been a joint custody arrangement.
The Associated Press contributed to this report.
