Murphy, 46, took the test on Monday at a Beverly Hills medical facility. "Eddie came in half an hour after Mel B. and the baby," says a source. "They didn't want to run into each other."
Results of the test could take anywhere from five days to three weeks.
Brown, 32, welcomed the baby, Angel Iris Murphy Brown, on April 3, and has long insisted Murphy is the child's father.
She and the comic dated last summer, but in December Murphy told a Dutch TV show of Brown's pregnancy: "I don't know whose child that is until it comes out and has a blood test."
In March, Murphy's current girlfriend, Tracey Edmonds, told Chicago's Power 92 radio station: "There'll be a paternity test and if it's [Eddie's] then he'll be responsible."
She also said Murphy also had not contacted her since Angel was born: "He hasn't seen his daughter. My people have contacted his people and they just had no response to anything."
When reached for comment by PEOPLE, Murphy's rep, Arnold Robinson, said at the time: "We do not comment on Mr. Murphy's personal life."