Rosdeep Adekoya "lost her temper" and beat the toddler after he was sick following a family day out at a restaurant in January.
Adekoya rained 40 blows on the young boy at their Edinburgh home.
Following the attack, a court heard, his life could have been saved had doctors been called in time.
However, he died from his injuries two days later and Adekoya put his body into a suitcase before driving 25 miles to Kirkaldy to hide it in woodland.
A major search was launched for Mikaeel after his mother called 999 and reported him missing in an effort to conceal her crime.
Hundreds of members of the public joined in the effort to find the boy.
However, mobile phone masts recorded the 34-year-old's journey across the Forth Road Bridge, in the first in a series of inconsistencies in her story to police.
She broke down under questioning, admitting: "It was an accident and I panicked."
Adekoya was charged with Mikaeel's murder but pleaded guilty to the reduced charge of culpable homicide at the High Court in Edinburgh.
She admitted a separate charge of attempting to defeat the ends of justice by pretending to police he had gone missing.
Defence QC Brian McConnachie said the case was "truly tragic" for all the family, adding: "Rosdeep Adekoya is not a monster."
Adekoya's internet history showed searches including, "I find it hard to love my son"; "Why am I so aggressive with my son"; and "Get rid of bruises".
Fife Council said it is holding a major review over the case, which it was overseeing.
Mikaeel died on the night of Tuesday, January 14, from injuries inflicted the previous Sunday.
He was smacked and punched on the body and head after vomiting repeatedly.
Adekoya dragged him to the shower by his arms and "beat him heavily" on his back as he lay over the bath edge, causing internal damage.
He was kept off nursery as his condition deteriorated and by Tuesday night he was "listless".
Advocate depute Alex Prentice said: "He would have been in significant pain but was put to bed.
"The pain would have increased significantly while Mikaeel became dangerously ill ... finally dying as a result of the injuries inflicted upon him by the accused.
"The accused discovered his body on the floor when wakening the children in the morning."
Adekoya put her son's body in a suitcase which she carried to the boot of her car, before taking his twin sister to nursery.
Mr Prentice added: "If medical assistance had been called for, death might not have resulted."
Mr McConnachie said: "This has been a brief period when this young woman has lost her temper and behaved in a way which is totally out of character for her".
She would have to live with the consequences for the rest of her life, he said.
Neighbour Paul Cairns, 46, who was involved in the search for Mikaeel, said: "The whole community came together [to search] and then, to be told that he had been killed... there would be a lot of angry people out there. I know that I'm one of them. The wee lad never had a chance to start off with."
Police Scotland Assistant Chief Constable Malcolm Graham, of Major Crime and Public Protection, said: "Mikaeel's disappearance and death deeply impacted on his family. It also resonated across the community in which he lived.
"Resources from across Police Scotland were deployed in the search for Mikaeel. Over two days officers were joined by members of the public in trying to find any trace of him.
"Sadly, our inquiries led us to Kirkcaldy the night after he was reported missing and the discovery of his body."
Sentence was deferred until August 25.