Watkins and his wife, Judy, led the procession from the church of the Rev. Corey Brooks, who has served as a spokesman for the Watkins family since the shooting.
Dressed in pink, Jonylah lay in a 3-foot-long casket that was flanked by floral arrangements spelling out "Mom" and "Dad." Next to the "Dad" arrangement was a poster with a drawing of Jonylah that said: "God's Angel: Jonylah Watkins."
Mourners streamed into the church and walked by Jonylah's casket as the songs "Take Me to the King" by Tamela Mann, "For You I Will" by Monica, and Whitney Houston's version of "I Will Always Love You," played in the background.
Many joined Jonathan Watkins in wearing pink in memory of Jonylah, whom her father called "Smooch" for "many kisses." Some were wearing clothing adorned with the baby's smiling face.
Jonylah was shot the afternoon of March 11 while with her dad in a minivan parked in the 6500 block of South Maryland Avenue. After extensive surgery, she died the next morning.
The gunman fled and is still at large. Police have said Jonathan Watkins, who also was shot, was the target of the ambush.
The service was both a joyous celebration of the baby's short life and a glaring light on the devastation Chicago violence has wrought on its victims.
In his eulogy, Brooks related how attached he had become to the Watkins family in the last week and said that Jonathan Watkins, who police have said is a member of the Gangster Disciples, told him he would embrace a church life.
Brooks appealed to Jonylah's parents, churchgoers, non-churchgoers, and "gangbangers in the room," saying terrible events like Jonylah's death could move people to change for the better.
"I want to challenge you to get clean," Brooks told the crowd. "Just because you are in dirty places and are with dirty people doesn't mean you have to be dirty."
Earlier, Jonylah's grandma, Mary Young, stood beside the baby's mother, Judy Watkins, and read a poem speaking out against violence.
"Our youth is in danger on the streets of this town with the forced code of silence while they shoot each other down," a section of the poem read.
The service also featured words from Ald. Willie Cochran (20th), who said that "Somebody is going to pay for this child."
Both Rabbi Michael Siegel of Lakeview's Anshe Emet Synagogue and the Rev. Marshall Hatch, pastor of New Mount Pilgrim Missionary Baptist Church in West Garfield Park, noted that Jonylah's death resonates beyond Woodlawn.
"All of us need to apologize to her for not doing our best to make this world a better place," Hatch said. "There is power in the blood of the innocent. If the blood of this baby does not change our lives, our lives are beyond change."
Jonylah's slaying drew national attention, and even those who'd never met her said her death touched their lives.
"When I heard about the shooting, I looked at my niece, I went home and cried," said Woodlawn resident Allen Lumpkin, 49, who stood outside the church Tuesday morning. Lumpkin said didn't know the family but felt the need to attend Jonylah's funeral.
Woodlawn resident Pershall Mitchell, 38, who knows the Watkins family, said, "It's important for all of us to come together and support the family. Her death melted my heart."
On Monday night, hundreds came to Leak and Sons Funeral Home to view Jonylah's tiny body as she lay dressed in pink with white-and-brown shoes.