Sara Ege, 33, beat Yaseen Ege to death at their home in Pontcanna, Cardiff, in July 2010 and set fire to his body.
She was also found guilty of perverting the course of justice at Cardiff Crown Court. Sentence was adjourned.
The boy's father, Yousuf Ege, 38, was acquitted of causing Yaseen's death by failing to protect him.
Yaseen Ege was beaten to death by his mother, who then set fire to his body
It was initially thought Yaseen had died in the blaze at the family home but tests later revealed he had died hours earlier.
His mother had pleaded not guilty to his murder and claimed her husband was responsible for Yaseen's death.
She said she feared her husband would murder her unless she confessed to the murder.
That confession - made to police days after the death of her son - was captured on video and played to the jury during the five week trial.
During the hour-long harrowing footage, Ege described how the young boy collapsed while still murmuring extracts of the Koran.
"He was breathing as if he was asleep when I left him," she said.
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Sara Ege made no attempt to seek the medical attention he so obviously needed”
"He was still murmuring the same thing over and over again. I thought that he was just tired."
When she returned 10 minutes later she found her son shaking and shivering on the floor. He then died.
Within moments she said she decided to burn his body and ran downstairs to get a lighter and a bottle of barbecue gel.
In police interviews she also confessed to beating her son for no reason and that her anger often led to her being out of control.
"It was not my intention to do anything. I cannot explain, I loved my son so much," she told officers.
"He was so good. He never, ever complained about anything."
The prosecution said that Yaseen suffered significant abdominal injuries that were the cause of his death.
Emergency services at the house in Pontcanna in 2010
They included fractures which were non-accidental.
"Sara Ege made no attempt to seek the medical attention he so obviously needed," prosecutor Ian Murphy said.
"He clearly suffered terribly. She started the fire to hide what she had done."
Ege was found guilty of murder and perverting the course of justice by burning Yaseen's body.
Her husband was cleared of causing or allowing the death of a child by failing to protect him.
The jury returned unanimous verdicts after eight hours of deliberation.
As the verdict was read out Ege broke down in the dock, holding her head in her hands and crying.
Judge Mr Justice Wyn Williams told her she faces a term of life imprisonment
Her husband showed no emotion as he walked free from court.
Mr Justice Wyn Williams told the court he would determine a minimum sentence for Ege in the New Year after a medical report had been completed.