Yesenia was sleeping inside her home on the 500 block of York Street when police say the suspects started shooting at her house.
Police believe the suspects mistakenly targeted the wrong home in retaliation for a prior incident.
Detectives have had the pair under surveillance for some time. They finally made their move Thursday afternoon.
Officers arrested Crawford in Fairfield after 3 p.m. they arrested McNeal a few hours later in Vallejo.
"When this incident first broke many of our officers were distraught, especially being that it was a 3-year-old baby girl who was completely innocent and uninvolved in any of this and for her to sustain such a serious injury it really affected our officers," Vallejo Police Department spokesperson Lieutenant Kenny Park said.
Officers say Yesenia is able to walk now, but with a limp. The bullet is still lodged in her spine and she is said to be in a lot of pain.
Those close to Yesenia say she continues to have nightmares and often wakes up screaming.
Police say the two men accused of shooting her are being booked on suspicion of attempted murder.