The baby and the 31-year-old woman's 5-year-old daughter were taken into protective custody, police said.
The handgun was not loaded, and a search conducted by a bomb-sniffing dog found no explosives, police said.
"The female suspect will be booked into jail on the appropriate criminal charges which will include making criminal threats and displaying a handgun in a threatening manner," San Diego police said in a statement.
The sermon at the non-denominational Church TsidKenu was about to conclude when the woman walked on stage, the San Diego Union-Tribune reported, citing pastor Ben Wisan.
As people in church approached the woman, she pointed her gun at them and the baby, ordering people not to come any closer, the Union-Tribune said, citing witness comments to OnScene TV.
"Members of the congregation were able to subdue her and get the gun away from her. Police arrived moments later and were able to take her into custody," San Diego Police Sergeant Robert Hawkins said, according to the Times of San Diego website.
San Diego police had previously announced they would have extra patrols of churches following the bombing of churches in Sri Lanka that killed more than 200 people and injured at least 450.