David Roberts said the child's ability to breathe was compromised by an "unsafe" sleeping environment after her father Paul Worthington took her from her cot and placed her next to him in his bed.
Mr Roberts said 13-month-old Poppi was suffering from an upper respiratory tract infection at the time and she was abused in the bed.
The Crown Prosecution Service says it does not plan to review its decision not to charge Mr Worthington.
At Kendal Coroner's Court, Mr Roberts concluded she did not die immediately after the abuse in 2012 and it did not cause her death.
The coroner said an unlawful killing conclusion was not available to him as he was not satisfied beyond reasonable doubt that Poppi died due to murder or manslaughter.
During a three-week inquest in Cumbria, Mr Worthington refused to answer questions about her death 252 times and his account did not "stand up to scrutiny", according to the coroner.
A family court judge ruled in January 2016 that "on the balance of probabilities" he had sexually assaulted Poppi before she died.
The father has denied any wrongdoing and has not been charged with any offence as the Crown Prosecution Service says there is insufficient evidence.
He has been living in hiding since the family court proceedings were made public.
The inquest at Kendal Coroner's Court was told the child woke up screaming at about 5.30am on 12 December 2012, at her home in Barrow-in-Furness and her father put her in his bed and went to get a fresh nappy.
Mr Worthington said that when he returned, she had settled but 5-10 minutes later he reached over and she was limp.
He claimed he then ran downstairs and the child's mother, who was sleeping downstairs, called an ambulance.
Paramedics took the youngster to Furness General Hospital at 6.11am but she never regained consciousness and was pronounced dead shortly after 7am.
The pathologist who carried out Poppi's post-mortem examination found Poppi's injuries, including two fractures to her leg, to be strongly suspicious of child abuse.
Poppi's mother, who cannot be named for legal reasons, looked red-eyed and close to tears for much of Monday's three-hour hearing.
After the inquest, her lawyer Fiona McGhie told reporters: "The past five years have been a complete nightmare for my client.
"Now knowing what happened to Poppi on that day and knowing that there were evidence-gathering failures by police in the very early stages of the investigation has made things worse.
"She is disappointed that Poppi's father chose to rely on his right not to answer questions which might incriminate him. While she understands he is entitled to do this, she considers he should have given the coroner the crucial evidence of Poppi's last few hours."
Paul Worthington's sister Tracy told Sky News: "He has been through so much and he's done nothing wrong and he doesn't know which way to turn. He can only go on the advice of his solicitors."
Cumbria Police chief constable Jerry Graham said he would discuss the case with the Crown Prosecution Service to "determine possible courses of action".
Mr Worthington's solicitors said the father was "considering his options", adding that "we are advising him not to say anything further at this point".
Background to the case, by Sky Correspondent Sally Lockwood
The inquest in Kendal heard three weeks of evidence from nearly 40 witnesses including Poppi's parents, Cumbria police who failed to properly investigate, and medical experts with conflicting views on what happened to the toddler.
Poppi's father
Poppi's father, Paul Worthington, was the key witness at this inquest after a family court judge ruled in January 2016 that "on the balance of probabilities" he had sexually assaulted Poppi before she died.
Paul Worthington has always denied this and has never been charged with any offence.
During his two days of evidence where he was screened from the public gallery, Mr Worthington refused to answer 252 questions.
Instead, he referred to his right under rule 22 of the Coroners and Justice Act, not to answer any questions that might incriminate him.
He sobbed in court as he was asked if he had sexually abused Poppi.
Swabs taken from Worthington after her death found his daughter's DNA on his penis. A forensic scientist who tested it found the location of the DNA "tends to exclude" the possibility he had assaulted her. Mr Worthington's lawyers explained the DNA had been transferred from his hands when he went to the toilet.
Poppi's mother
Poppi's mother, who has been granted anonymity for legal reasons, told the inquest Poppi had seemed unwell the day before she died, with a possible belly ache.
The court heard she was asleep on the sofa downstairs that night when she heard Poppi cry out. She said the noise was louder than her normal cries, "more of a scream".
Shortly after Paul Worthington came downstairs to get a nappy. Then at 6am she was awoken by Mr Worthington calling for her to get an ambulance because Poppi had stopped breathing.
Conflicting medical evidence
Poppi was taken to Furness General Hospital where suspicion was first raised by consultant paediatrician Dr Osama Braima who found Poppi to be bleeding from her anus.
Dr Braima told the inquest he was suspicious and alerted children's services. The pathologist who carried out Poppi's post-mortem examination found Poppi's injuries, including two fractures to her leg, to be strongly suspicious of child abuse.
Dr Alison Armour, who found no natural cause of death, told the court the tiny tears in Poppi's bottom and the fact it was "dilated" were of particular concern.
Other experts strongly disagreed with her interpretation of the findings. Dr Nat Cary, a former Home Office pathologist, said the condition of Poppi's bottom was a common phenomenon in child deaths.
Police failings
This inquest is particularly challenging for the coroner due to the loss of evidence in the investigation carried out by Cumbria Police.
Officers had "no search strategy" when seizing crucial evidence, the inquest heard.
Retired Cumbria Police detective superintendent Cath Thundercloud described a series of failures committed when officers visited the family home in Barrow following Poppi's death.
She admitted officers failed to carry out even "common sense" checks.
Former Detective Constable Lindsey Bolton, who is no longer a serving police officer, said the laptop used by Mr Worthington to watch pornography the night that Poppi died was never recovered by officers.
Head of the investigation, former Det Insp Amanda Sadler, admitted to the the court she had not had full training or enough experience to do the job.
The errors mean it is unlikely anyone will ever be prosecuted over Poppi's death because the Crown Prosecution Service has twice ruled there is insufficient evidence.
Representing Poppi's mother, Gillian Irving QC said: "If this was not such a tragedy one could best describe the response of Cumbria Constabulary as a comedy of errors."
Ms Irving agreed with Mr Worthington's lawyer, Leslie Thomas QC, that neither a conclusion of unlawful killing nor natural causes was open to the coroner.