Police in the area have charged a man with attempted murder after the incident on Sunday morning at Oasis Tabernacle Church in East Selma.
The baby's father James Junior Minter, 26, is accused of the attack which officers say is related to a 'domestic incident'.
It was not a racist attack, police added.
"The mother is in critical condition. She and the baby were sent to Birmingham for medical treatment. The pastor is at a local hospital in Selma," Dallas County District Attorney Michael Jackson told CNN.
Police said the pastor was shot as he tried to wrestle the gun from the shooters hands.
The woman was shot in the shoulder and jaw whilst the child was shot in the hand shortly after they entered the church.
A man fled the scene but was caught by officers soon afterwards.
