Koman Willis, 33, was charged with first degree murder and aggravated battery with a firearm in the baby's slaying, police said. Willis is a documented gang member with 38 prior arrests, according to cops.
Willis turned himself in over the weekend but declined to provide a statement, police said.
"He knew we were out looking for him," McCarthy said.
Police said Jonylah's father, Jonathan Watkins, robbed Willis of a video game system prior to the shooting, which prompted the attack in which he and his daughter were shot.
Jonathan Watkins, not Jonylah, was the intended target to the fatal shooting, police said.
No weapon has been recovered, but McCarthy said witness accounts corroborated the evidence police had recovered. Pictures of the shooter's van leaving the scene also contributed to what police said is the evidence that finally pinned Willis.
"I don't want to use cliche terms, but police were pounding the pavement [on this case]," McCarthy said.
In a case that shocked the city and the nation, Jonylah Watkins was killed March 11 while on her father's lap in a car in the 6500 block of South Maryland Avenue.
Initial reports said Jonathan Watkins was changing her diaper when a gunman fired at him, striking Watkins twice. Jonylah was hit once, but suffered multiple wounds.
Jonylah's death rattled a city already under duress following a bloody 2012 that saw more than 500 people murdered, and just weeks after 15-year-old Hadiya Pendleton was gunned down about a mile from President Obama's Kenwood home.
During an impromptu news conference Sunday, Pastor Corey Brooks stood with Jonathan and Judy Watkins outside New Beginnings Church, saying the family "believes real soon that someone will be charged."
"We talk to the police every day, so this has been like any other day for us," Brooks said.
Brooks, who has spoken on behalf of the Watkins family since their baby was killed three months ago, said the couple spent Memorial Day at Jonylah's grave site.
Brooks said that Jonathan Watkins has since gotten a job and is pursuing his GED in order to provide for his family during these tough times.
"We've seen support turn — we've seen a lot of people get behind him," Brooks said of Watkins, who was trounced by the media following news of his criminal past.
Police and Brooks said Monday that Watkins had been cooperating with police fully in their investigation.
The Watkins family is expected to speak out for the first time about the death of their young daughter Tuesday afternoon.
"If we have anything to say to the whole city of Chicago, it would just be 'thank you,'" Brooks said.