Prosecutors said Khalil's body was covered with scars, so many the medical examiner characterized them as "too numerous to put a number on."
He had at least 15 scars on his face.
First Assistant District Attorney Edward McCann said the verdict should have been harsher.
"I think we got a fair trial in front of a fair judge, but I do believe that we put on evidence of a first-degree case," McCann said.
La Reine Nixon, Khalil's foster grandmother, said she was "disappointed about the third degree. We were hoping for first-degree murder."
She said others also should be blamed for the child's death.
"Tina and Floyd should not be the only two who were on trial for his death. But for the judges in Family Court and DHS, Khalil would still be alive. In my opinion, they are as responsible, if not more so, because these people did what they do," Nixon said.
"They had  children and didn't raise any of them, and so it was obvious that they would not have done the right thing by him. And we specifically asked that Khalil not be a sacrificial lamb, for years."
The couple had been on the Department of Human Services' radar for a long time: The agency had already removed seven children from their custody.
"For years, we asked DHS and the courts not to turn this child over to these people and they did. So they are culpable and equally responsible," Nixon said.
Until he was 3, Khalil lived with his foster parents, Alicia Nixon-James and her then-husband, J. Evans.
Records show that in 2009, over strong objections from Nixon-James and Evans, Khalil's social worker and court-appointed child advocate, the youngster was returned to his parents.
Wimes and Cuffie had met the three conditions necessary to regain custody of Khalil: They had passed three drug tests; rented an apartment, at 22d Street near McClellan Street; and had taken parenting classes.
DHS monitored Khalil for a year after he went to live with his parents, and he was healthy during that period.
McCann said that immediately after the monitoring stopped in 2010, Wimes and Cuffie began to abuse the boy.
Cuffie told police she beat the boy with a belt almost every day, would sometimes make him stand facing a corner and throw books at him, and would punish him by forcing him to do push-ups and sit-ups and run back and forth in their apartment.
Investigators said the sickly boy slept on a soiled plastic mattress on the floor of a latched and squalid empty bedroom.
In the last eight months of Khalil's life, a DHS worker assigned to two of the boy's siblings spent time with Khalil during eight supervised visits at a DHS facility and the family's home.
The worker saw Khalil two weeks before the child's death but failed to notice that he was in serious danger. The worker has since been placed on desk duty.
On Thursday, Alicia Nixon-James testified that in her care, Khalil had been a healthy, chubby-cheeked tot who enjoyed riding a rocking horse on his second birthday.
After Friday's hearing, Nixon-James, in tears, declined to comment.
After the verdict, McCann said, "There was literally not a surface of this child's body that was not covered with an injury. He was whipped, he was beaten with belts, he was beaten with fists, and he was horribly emaciated. . . . It's as bad as it gets . . . in terms of child abuse.
"The most haunting thing for me will be that this child did not have to die this way. This child was well cared for. He was a beautiful young boy at the age of 3, thriving. . . . By July of 2011, they had already killed him, if you look at the pictures of him at that time."
McCann said the third-degree murder conviction carries a maximum sentence of 331/2 years to 67 years in prison. Sentencing is scheduled for Nov. 26.