The verdict was a blow to prosecutors who had portrayed Rodriguez as a depraved disciplinarian who killed Nixzmary over some missing yogurt.
"We would have liked to up the charge," said one juror, Terrence Cobwell. "But the prosecution didn't really give us enough."
Deliberations, which spanned four days, were tense, Cobwell added. "I mean, the whole trial was tense. ... We just wanted justice for the little girl."
Rodriguez, 29, also was convicted of endangering the welfare of a child and criminal possession of a weapon, including a belt used to beat Nixzmary.
He listened to the verdict with a bowed head but showed no sign of emotion. Sentencing is set for April 3.
Defense attorney Jeffrey Schwartz -- architect of a brazen strategy casting Nixzmary as a troublemaker and her mother as the real culprit -- said his client was disappointed and would appeal.
"I hope he keeps praying and staying strong," the lawyer said.
Prosecutor Ama Dwimoh conceded that the state had failed to convince the jury that Rodriguez had acted with "depraved indifference" -- the standard for second-degree murder -- instead of mere recklessness in killing Nixzmary, whose body was found on Jan. 11, 2006.
"I am grateful that at least they're holding him accountable with a manslaughter conviction," Dwimoh said.
Evidence in the nearly three-month-long trial in state Supreme Court included grim crime scene photos from the room where Nixzmary was bound to a chair, starved and forced to urinate in a litter box. More than once, court officers passed out tissues so weeping jurors could dry their eyes.
The prosecution also relied heavily on a videotaped statement in which Rodriguez said that on the little girl's last night, he caught her stealing yogurt and decided to punish her by sticking her head under running bath water "to make her think."
Investigators suspect the girl's head was smashed against the faucet -- something her stepfather denied doing.
Rodriguez admitted he had abused the little girl but denied killing her, saying on tape, "Sometimes she'd get me real angry, and I used to just throw her on the floor. ... She was always lying to me about everything."
In closing arguments, Dwimoh displayed a large photo of the victim's body -- bruised, topless and splayed on a wooden floor in the family's ramshackle apartment -- as she stood in front of the defense table and berated Rodriguez.
"You battered a little girl who weighed 36 pounds," she said last week. "When she was on the floor in that room you imprisoned her in, you turned your back."
Schwartz countered by labeling Nixzmary's mother a violent and vengeful "Mommy Dearest."
He also portrayed the victim as a violent and uncontrollable "little Houdini" -- a reference to her supposed knack at slipping out of the makeshift restraints devised by her parents to keep her from attacking her younger siblings.
The defense asked the jury to focus on the testimony of a jail inmate who claimed that behind bars the mother, Nixzaliz Santiago, described a fatal beating. The mother faces a separate trial later this year on murder charges.
It was "the confession of the sick, of the demented, of the disturbed mother," Schwartz said.
Schwartz also sought to blame the city's overburdened Administration for Children's Services for doing too little to intervene. Though school employees had reported that Nixzmary had been absent for weeks the previous year and neighbors noticed unexplained injuries, child welfare workers said they found no conclusive evidence of abuse.
The case, coupled with a series of other high-profile deaths of children known to the agency, sparked public demands for reform. City officials responded by bolstering the corps of caseworkers.
Five bills in the Legislature inspired by Nixzmary's case are stuck in committee. Most would increase punishment for child-abuse crimes or make it easier for police to intervene.
